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Merge pull request #101 from galaxyproject/review-snippets
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Minor improvements in Snippets
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@davelopez
davelopez authored Jan 23, 2021
2 parents f4489e5 + 2af30d6 commit 5b74c55
Showing 1 changed file with 47 additions and 28 deletions.
75 changes: 47 additions & 28 deletions client/src/snippets.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2,40 +2,59 @@
"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 -->",
" <!-- 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>",
" </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)",
"",
".. class:: infomark",
"",
"**What it does**",
"",
"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",
".....",
"",
"",
"**Input**",
"",
"",
"**Output**",
"",
"",
" ]]></help>",
" <citations>",
" <citation type=\"doi\"></citation>",
" <citation type=\"doi\"> </citation>",
" </citations>",
"</tool>"
],
Expand All @@ -45,9 +64,9 @@
"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=\"$3\" help=\"${4:TODO}\">",
" <option value=\"$5\">TODO: $5</option>",
" <option value=\"$6\">TODO: $6</option>",
" </param>",
" <when value=\"$5\">",
" $0",
Expand All @@ -61,66 +80,66 @@
"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=\"$2\" help=\"${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"
},
"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=\"$2\" help=\"${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"
},
"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"
},
"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\" name=\"$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\" 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: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=\"_\" />",
Expand All @@ -140,7 +159,7 @@
" <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\" />",
Expand All @@ -149,7 +168,7 @@
" </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>"
],
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