From fbee6202c4ca07539b7f8c77034e6c46ccb8c528 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sat, 23 Jan 2021 18:34:36 +0100
Subject: [PATCH 1/9] Simplify snippet filling

The `help` attribute now is directly replaced by a `TODO` (instead of a regular placeholder) because it should require considerable time to fill in this attribute and may break the 'speed' of the placeholder editing.
---
 client/src/snippets.json | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/client/src/snippets.json b/client/src/snippets.json
index 8d208c5..8785dc4 100644
--- a/client/src/snippets.json
+++ b/client/src/snippets.json
@@ -45,14 +45,14 @@
         "prefix": "gx-conditional-select",
         "body": [
             "<conditional name=\"$1\">",
-            "    <param name=\"$2\" type=\"select\" label=\"$3\" help=\"$4\">",
-            "        <option value=\"$5\">TODO: option $5</option>",
-            "        <option value=\"$6\">TODO: option $6</option>",
+            "    <param name=\"$2\" type=\"select\" label=\"$3\" help=\"TODO\">",
+            "        <option value=\"$4\">TODO: $4</option>",
+            "        <option value=\"$5\">TODO: $5</option>",
             "    </param>",
-            "    <when value=\"$5\">",
+            "    <when value=\"$4\">",
             "        $0",
             "    </when>",
-            "    <when value=\"$6\">",
+            "    <when value=\"$5\">",
             "    </when>",
             "</conditional>"
         ],
@@ -61,10 +61,10 @@
     "Select parameter with 3 options": {
         "prefix": "gx-select-3-param",
         "body": [
-            "<param name=\"$1\" type=\"select\" label=\"$2\" help=\"$3\">",
-            "    <option value=\"$4\">TODO: option $4</option>",
-            "    <option value=\"$5\">TODO: option $5</option>",
-            "    <option value=\"$6\">TODO: option $6</option>",
+            "<param name=\"$1\" type=\"select\" label=\"$2\" help=\"TODO\">",
+            "    <option value=\"$3\">TODO: $3</option>",
+            "    <option value=\"$4\">TODO: $4</option>",
+            "    <option value=\"$5\">TODO: $5</option>",
             "</param>"
         ],
         "description": "Select parameter with 3 options"
@@ -72,12 +72,12 @@
     "Select parameter with 5 options": {
         "prefix": "gx-select-5-param",
         "body": [
-            "<param name=\"$1\" type=\"select\" label=\"$2\" help=\"$3\">",
-            "    <option value=\"$4\">TODO: option $4</option>",
-            "    <option value=\"$5\">TODO: option $5</option>",
-            "    <option value=\"$6\">TODO: option $6</option>",
-            "    <option value=\"$7\">TODO: option $7</option>",
-            "    <option value=\"$8\">TODO: option $8</option>",
+            "<param name=\"$1\" type=\"select\" label=\"$2\" help=\"TODO\">",
+            "    <option value=\"$3\">TODO: $3</option>",
+            "    <option value=\"$4\">TODO: $4</option>",
+            "    <option value=\"$5\">TODO: $5</option>",
+            "    <option value=\"$6\">TODO: $6</option>",
+            "    <option value=\"$7\">TODO: $7</option>",
             "</param>"
         ],
         "description": "Select parameter with 5 options"

From aa096a0c7b5dec9bc3c0c0d22f44dce280346f6c Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sat, 23 Jan 2021 18:37:36 +0100
Subject: [PATCH 2/9] Add dashes to arguments and remove name attribute

By default all `param` snippets include only the `argument` attribute instead of the `name`.
---
 client/src/snippets.json | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/client/src/snippets.json b/client/src/snippets.json
index 8785dc4..fea6bcf 100644
--- a/client/src/snippets.json
+++ b/client/src/snippets.json
@@ -85,42 +85,42 @@
     "Boolean parameter": {
         "prefix": "gx-boolean-param",
         "body": [
-            "<param argument=\"$1\" type=\"boolean\" truevalue=\"$1\" falsevalue=\"$2\" label=\"$3\" help=\"$4\" />"
+            "<param argument=\"--$1\" type=\"boolean\" truevalue=\"$1\" falsevalue=\"$2\" label=\"$3\" help=\"$4\" />"
         ],
         "description": "Boolean parameter"
     },
     "Integer parameter": {
         "prefix": "gx-integer-param",
         "body": [
-            "<param argument=\"$1\" type=\"integer\" min=\"$2\" max=\"$3\" value=\"$4\" label=\"$5\" help=\"$6\" />"
+            "<param argument=\"--$1\" type=\"integer\" min=\"$2\" max=\"$3\" value=\"$4\" label=\"$5\" help=\"$6\" />"
         ],
         "description": "Integer parameter"
     },
     "Float parameter": {
         "prefix": "gx-float-param",
         "body": [
-            "<param argument=\"$1\" type=\"float\" min=\"$2\" max=\"$3\" value=\"$4\" label=\"$5\" help=\"$6\" />"
+            "<param argument=\"--$1\" type=\"float\" min=\"$2\" max=\"$3\" value=\"$4\" label=\"$5\" help=\"$6\" />"
         ],
         "description": "Float parameter"
     },
     "Data parameter with single required dataset": {
         "prefix": "gx-data-single-param",
         "body": [
-            "<param argument=\"$1\" name=\"$1\" type=\"data\" format=\"$2\" label=\"$3\" help=\"$4\" />"
+            "<param argument=\"--$1\" type=\"data\" format=\"$2\" label=\"$3\" help=\"$4\" />"
         ],
         "description": "Data parameter with single required dataset"
     },
     "Data parameter with multiple required datasets": {
         "prefix": "gx-data-multiple-param",
         "body": [
-            "<param argument=\"$1\" name=\"$1\" type=\"data\" format=\"$2\" multiple=\"true\" label=\"$3\" help=\"$4\" />"
+            "<param argument=\"--$1\" type=\"data\" format=\"$2\" multiple=\"true\" label=\"$3\" help=\"$4\" />"
         ],
         "description": "Data parameter with multiple required datasets"
     },
     "Text parameter": {
         "prefix": "gx-text-param",
         "body": [
-            "<param argument=\"$1\" type=\"text\" value=\"$2\" label=\"$3\" help=\"$4\">",
+            "<param argument=\"--$1\" type=\"text\" value=\"$2\" label=\"$3\" help=\"$4\">",
             "    <sanitizer invalid_char=\"\">",
             "        <valid initial=\"string.letters,string.digits\">",
             "            <add value=\"_\" />",
@@ -140,7 +140,7 @@
             "        <option value=\"history\">History</option>",
             "    </param>",
             "    <when value=\"cached\">",
-            "        <param argument=\"$1\" type=\"select\"",
+            "        <param argument=\"--$1\" type=\"select\"",
             "            label=\"Reference genome\">",
             "            <options from_data_table=\"fasta_indexes\">",
             "                <filter type=\"data_meta\" column=\"dbkey\" key=\"dbkey\" ref=\"reads\" />",
@@ -149,7 +149,7 @@
             "        </param>",
             "    </when>",
             "    <when value=\"history\">",
-            "        <param argument=\"$1\" type=\"data\" format=\"fasta\" label=\"Reference\" help=\"Reference sequence\" />",
+            "        <param argument=\"--$2\" type=\"data\" format=\"fasta\" label=\"Reference\" help=\"Reference sequence\" />",
             "    </when>",
             "</conditional>"
         ],

From cb293e11055dda9438493514be526ffa9c5cb94a Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sat, 23 Jan 2021 18:46:07 +0100
Subject: [PATCH 3/9] Add default values to avoid self-closing on document save

---
 client/src/snippets.json | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/client/src/snippets.json b/client/src/snippets.json
index fea6bcf..7cc87db 100644
--- a/client/src/snippets.json
+++ b/client/src/snippets.json
@@ -14,10 +14,10 @@
             "    <!-- TODO: please annotate this tool with topics and operations from http://edamontology.org -->",
             "    <!-- TODO: for more information see: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#edam-topics-and-operations -->",
             "    <edam_topics>",
-            "        <edam_topic></edam_topic>",
+            "        <edam_topic>topic_TODO</edam_topic>",
             "    </edam_topics>",
             "    <edam_operations>",
-            "        <edam_operation></edam_operation>",
+            "        <edam_operation>operation_TODO</edam_operation>",
             "    </edam_operations>",
             "    <requirements>",
             "        <requirement type=\"package\" version=\"@TOOL_VERSION@\">$1</requirement>",
@@ -35,7 +35,7 @@
             "        TODO: Fill in help in reStructuredText (https://en.wikipedia.org/wiki/ReStructuredText)",
             "    ]]></help>",
             "    <citations>",
-            "        <citation type=\"doi\"></citation>",
+            "        <citation type=\"doi\"> </citation>",
             "    </citations>",
             "</tool>"
         ],

From 57be066209eb539c1f67b3e73757b55cfdb33a2e Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sat, 23 Jan 2021 18:46:51 +0100
Subject: [PATCH 4/9] Reorder placeholders

---
 client/src/snippets.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/snippets.json b/client/src/snippets.json
index 7cc87db..7db9662 100644
--- a/client/src/snippets.json
+++ b/client/src/snippets.json
@@ -2,13 +2,13 @@
     "Basic Galaxy tool": {
         "prefix": "gx-tool",
         "body": [
-            "<tool id=\"$1\" name=\"$2\" version=\"@TOOL_VERSION@+galaxy@VERSION_SUFFIX@\" profile=\"20.01\" license=\"${4|MIT,Apache-2.0,GPL-3.0-or-later,GPL-2.0-only,BSD-3-Clause,LGPL-3.0+|}\">",
+            "<tool id=\"$1\" name=\"$2\" version=\"@TOOL_VERSION@+galaxy@VERSION_SUFFIX@\" profile=\"20.01\" license=\"${3|MIT,Apache-2.0,GPL-3.0-or-later,GPL-2.0-only,BSD-3-Clause,LGPL-3.0+|}\">",
             "    <description>$5</description>",
             "    <xrefs>",
             "        <xref type=\"bio.tools\">$0</xref>",
             "    </xrefs>",
             "    <macros>",
-            "        <token name=\"@TOOL_VERSION@\">${3:0.1.0}</token>",
+            "        <token name=\"@TOOL_VERSION@\">${4:0.1.0}</token>",
             "        <token name=\"@VERSION_SUFFIX@\">0</token>",
             "    </macros>",
             "    <!-- TODO: please annotate this tool with topics and operations from http://edamontology.org -->",

From 5fbbf9d4b137c5b10205f6602144af0ea41d2c3a Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sat, 23 Jan 2021 18:51:01 +0100
Subject: [PATCH 5/9] Add some hints in the comments

---
 client/src/snippets.json | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/client/src/snippets.json b/client/src/snippets.json
index 7db9662..32fa1f7 100644
--- a/client/src/snippets.json
+++ b/client/src/snippets.json
@@ -23,13 +23,15 @@
             "        <requirement type=\"package\" version=\"@TOOL_VERSION@\">$1</requirement>",
             "    </requirements>",
             "    <command detect_errors=\"exit_code\"><![CDATA[",
-            "        TODO: Fill in command template.",
+            "        ## TODO: Fill in command using Cheetah templates",
+            "        ## Hint: Use [ctrl+alt+c] after defining the inputs/outputs to auto-generate some Cheetah boilerplate code for you.",
             "    ]]></command>",
             "    <inputs>",
             "    </inputs>",
             "    <outputs>",
             "    </outputs>",
             "    <tests>",
+            "        <!-- Hint: You can use [ctrl+alt+t] after defining the inputs/outputs to auto-scaffold some basic test cases. -->",
             "    </tests>",
             "    <help><![CDATA[",
             "        TODO: Fill in help in reStructuredText (https://en.wikipedia.org/wiki/ReStructuredText)",

From f2f5a747b49c4b4316e152db895f9701ec56d0a7 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sat, 23 Jan 2021 18:51:51 +0100
Subject: [PATCH 6/9] Include minimum help boilerplate

---
 client/src/snippets.json | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/client/src/snippets.json b/client/src/snippets.json
index 32fa1f7..0d2908e 100644
--- a/client/src/snippets.json
+++ b/client/src/snippets.json
@@ -34,7 +34,23 @@
             "        <!-- Hint: You can use [ctrl+alt+t] after defining the inputs/outputs to auto-scaffold some basic test cases. -->",
             "    </tests>",
             "    <help><![CDATA[",
-            "        TODO: Fill in help in reStructuredText (https://en.wikipedia.org/wiki/ReStructuredText)",
+            "",
+            ".. class:: infomark",
+            "",
+            "**What it does**",
+            "",
+            "TODO: Fill in help in reStructuredText format (https://en.wikipedia.org/wiki/ReStructuredText)",
+            "",
+            "Usage",
+            ".....",
+            "",
+            "",
+            "**Input**",
+            "",
+            "",
+            "**Output**",
+            "",
+            "",
             "    ]]></help>",
             "    <citations>",
             "        <citation type=\"doi\"> </citation>",

From 1412b4e5232727a3441f701e9c9b15c2f37c6f26 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sat, 23 Jan 2021 19:11:15 +0100
Subject: [PATCH 7/9] Add hint to reStructuredText online editor

---
 client/src/snippets.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/src/snippets.json b/client/src/snippets.json
index 0d2908e..23b4128 100644
--- a/client/src/snippets.json
+++ b/client/src/snippets.json
@@ -39,7 +39,8 @@
             "",
             "**What it does**",
             "",
-            "TODO: Fill in help in reStructuredText format (https://en.wikipedia.org/wiki/ReStructuredText)",
+            "TODO: Fill in help in reStructuredText format (https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html)",
+            "Hint: If you want, you can preview your help section using this online editor: http://rst.ninjs.org/",
             "",
             "Usage",
             ".....",

From 65fbf749090076a6198884e7460d2f9d62b5231d Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sat, 23 Jan 2021 19:18:14 +0100
Subject: [PATCH 8/9] Add dashes in boolean param as default value

---
 client/src/snippets.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/snippets.json b/client/src/snippets.json
index 23b4128..1eda33a 100644
--- a/client/src/snippets.json
+++ b/client/src/snippets.json
@@ -104,7 +104,7 @@
     "Boolean parameter": {
         "prefix": "gx-boolean-param",
         "body": [
-            "<param argument=\"--$1\" type=\"boolean\" truevalue=\"$1\" falsevalue=\"$2\" label=\"$3\" help=\"$4\" />"
+            "<param argument=\"${1:--}\" type=\"boolean\" truevalue=\"$1\" falsevalue=\"$2\" label=\"$3\" help=\"${4:TODO}\" />"
         ],
         "description": "Boolean parameter"
     },

From 2af30d608621de05cce51e6bdddf380a8cb2d5f6 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sat, 23 Jan 2021 19:19:58 +0100
Subject: [PATCH 9/9] Add TODO as default value for help attributes

---
 client/src/snippets.json | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/client/src/snippets.json b/client/src/snippets.json
index 1eda33a..d07a7f2 100644
--- a/client/src/snippets.json
+++ b/client/src/snippets.json
@@ -64,14 +64,14 @@
         "prefix": "gx-conditional-select",
         "body": [
             "<conditional name=\"$1\">",
-            "    <param name=\"$2\" type=\"select\" label=\"$3\" help=\"TODO\">",
-            "        <option value=\"$4\">TODO: $4</option>",
+            "    <param name=\"$2\" type=\"select\" label=\"$3\" help=\"${4:TODO}\">",
             "        <option value=\"$5\">TODO: $5</option>",
+            "        <option value=\"$6\">TODO: $6</option>",
             "    </param>",
-            "    <when value=\"$4\">",
+            "    <when value=\"$5\">",
             "        $0",
             "    </when>",
-            "    <when value=\"$5\">",
+            "    <when value=\"$6\">",
             "    </when>",
             "</conditional>"
         ],
@@ -80,10 +80,10 @@
     "Select parameter with 3 options": {
         "prefix": "gx-select-3-param",
         "body": [
-            "<param name=\"$1\" type=\"select\" label=\"$2\" help=\"TODO\">",
-            "    <option value=\"$3\">TODO: $3</option>",
+            "<param name=\"$1\" type=\"select\" label=\"$2\" help=\"${3:TODO}\">",
             "    <option value=\"$4\">TODO: $4</option>",
             "    <option value=\"$5\">TODO: $5</option>",
+            "    <option value=\"$6\">TODO: $6</option>",
             "</param>"
         ],
         "description": "Select parameter with 3 options"
@@ -91,12 +91,12 @@
     "Select parameter with 5 options": {
         "prefix": "gx-select-5-param",
         "body": [
-            "<param name=\"$1\" type=\"select\" label=\"$2\" help=\"TODO\">",
-            "    <option value=\"$3\">TODO: $3</option>",
+            "<param name=\"$1\" type=\"select\" label=\"$2\" help=\"${3:TODO}\">",
             "    <option value=\"$4\">TODO: $4</option>",
             "    <option value=\"$5\">TODO: $5</option>",
             "    <option value=\"$6\">TODO: $6</option>",
             "    <option value=\"$7\">TODO: $7</option>",
+            "    <option value=\"$8\">TODO: $8</option>",
             "</param>"
         ],
         "description": "Select parameter with 5 options"
@@ -111,35 +111,35 @@
     "Integer parameter": {
         "prefix": "gx-integer-param",
         "body": [
-            "<param argument=\"--$1\" type=\"integer\" min=\"$2\" max=\"$3\" value=\"$4\" label=\"$5\" help=\"$6\" />"
+            "<param argument=\"--$1\" type=\"integer\" min=\"$2\" max=\"$3\" value=\"$4\" label=\"$5\" help=\"${6:TODO}\" />"
         ],
         "description": "Integer parameter"
     },
     "Float parameter": {
         "prefix": "gx-float-param",
         "body": [
-            "<param argument=\"--$1\" type=\"float\" min=\"$2\" max=\"$3\" value=\"$4\" label=\"$5\" help=\"$6\" />"
+            "<param argument=\"--$1\" type=\"float\" min=\"$2\" max=\"$3\" value=\"$4\" label=\"$5\" help=\"${6:TODO}\" />"
         ],
         "description": "Float parameter"
     },
     "Data parameter with single required dataset": {
         "prefix": "gx-data-single-param",
         "body": [
-            "<param argument=\"--$1\" type=\"data\" format=\"$2\" label=\"$3\" help=\"$4\" />"
+            "<param argument=\"--$1\" type=\"data\" format=\"$2\" label=\"$3\" help=\"${4:TODO}\" />"
         ],
         "description": "Data parameter with single required dataset"
     },
     "Data parameter with multiple required datasets": {
         "prefix": "gx-data-multiple-param",
         "body": [
-            "<param argument=\"--$1\" type=\"data\" format=\"$2\" multiple=\"true\" label=\"$3\" help=\"$4\" />"
+            "<param argument=\"--$1\" type=\"data\" format=\"$2\" multiple=\"true\" label=\"$3\" help=\"${4:TODO}\" />"
         ],
         "description": "Data parameter with multiple required datasets"
     },
     "Text parameter": {
         "prefix": "gx-text-param",
         "body": [
-            "<param argument=\"--$1\" type=\"text\" value=\"$2\" label=\"$3\" help=\"$4\">",
+            "<param argument=\"--$1\" type=\"text\" value=\"$2\" label=\"$3\" help=\"${4:TODO}\">",
             "    <sanitizer invalid_char=\"\">",
             "        <valid initial=\"string.letters,string.digits\">",
             "            <add value=\"_\" />",