Merge pull request #125 from mthang/filsender_update

fix xml, add macros.xml and README

tools/aarnetfilesender/README.md

@@ -1,3 +1,26 @@
-# AARNet FileSender
+ENA-upload-cli wrapper
+======================
 
-This is a wrapper for AARNet's FileSender, using the FileSender CLI tool.
+Galaxy wrapper of the AARNET
+`filesender <https://support.aarnet.edu.au/hc/en-us/articles/230067927-Send-files-with-FileSender>`__.
+
+Setting up credentials on Galaxy
+--------------------------------
+
+The admin can enable users to set their own credentials
+for this tool. To enable it, make sure the file
+``config/user_preferences_extra_conf.yml`` has the following section:
+
+.. code-block:: yaml
+
+    aarnet_filesender_account:
+        description: AARNet FileSender Account Info
+        inputs:
+            - name: username
+              label: AARNet FileSender Username
+              type: text
+              required: False
+            - name: apikey
+              label: AARNet FileSender API Key
+              type: password
+              required: False

tools/aarnetfilesender/filesender.xml

@@ -1,23 +1,19 @@
-<?xml version="1.0"?>
-
-<tool id="aarnet_filesender" name="AARNet FileSender" version="3.0.0" workflow_compatible="true">
-    <requirements>
-        <requirement type="package" version="3.0.0">filesendercli</requirement>
-    </requirements>
+<tool id="aarnet_filesender" name="AARNet FileSender" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>transfer files to AARnet's FileSender Service</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
 #set $apiuser = $__user__.extra_preferences.get('aarnet_filesender_account|username', "").strip()
 #set $apikey = $__user__.extra_preferences.get('aarnet_filesender_account|apikey', "").strip()
 
-#if $apiuser == "":
+#if $apiuser == "" or $apikey == "":
     echo "ERROR: Please enter your FileSender Username in your user preferences under the AARNet FileSender Account Info section" &&
     exit 1;
 #end if
 
-#if $apikey == "":
-    echo "ERROR: Please enter your FileSender API Key in your user preferences under the AARNet FileSender Account Info section" &&
-    exit 1;
-#end if
-
 #if $to == "":
     echo "WARNING: recipent email not set, setting to $__user_email__" &&
     #set $to = $__user_email__
@@ -34,15 +30,27 @@ mkdir filestosend &&
 #end for
 
 filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/rest.php -f "[email protected]" -r '$to' filestosend >$output 2>&1
-
     ]]></command>
     <inputs>
-        <param name="data" type="data" multiple="true" optional="false" label="Datasets to be sent:" />
+        <param name="data" type="data" format="txt,data" multiple="true" optional="false" label="Datasets to be sent:" />
         <param name="to" type="text" optional="false" label="Email address of recipent:"><sanitizer sanitize="False"/></param>
     </inputs>
     <outputs>
         <data name="output" type="data" format="txt" hidden="false"/>
     </outputs>
+    <tests>
+         <!-- TODO planemo failed due to both username and apikey are null-->
+        <test>
+          <param name="data" value="summary_statistics.txt"/>
+             <output name="output">
+                     <assert_contents>
+                         <has_text text="Uploading"/>
+                         <has_text text="log complete"/>
+                         <has_text text="Upload Complete"/>
+                     </assert_contents>
+             </output>
+          </test>
+    </tests>
     <help>
 **What it does**
         Send dataset(s) from Galaxy to anyone via AARNet's FileSender service.

tools/aarnetfilesender/test-data/output.log

@@ -0,0 +1,3 @@
+Uploading: Xnatutils on data 2424: log 100%
+Xnatutils on data 2424: log complete
+Upload Complete

tools/aarnetfilesender/test-data/summary_statistics.txt

@@ -0,0 +1,5 @@
+Core genes	(99% <= strains <= 100%)	251
+Soft core genes	(95% <= strains < 99%)	0
+Shell genes	(15% <= strains < 95%)	0
+Cloud genes	(0% <= strains < 15%)	0
+Total genes	(0% <= strains <= 100%)	251