Mercurial > repos > nml > bundle_collections
diff bundle_collection.xml @ 2:705ebd286b57 draft default tip
"planemo upload commit 7761f1e59039279728185e751f1a51b56fe14cb0"
| author | nml |
|---|---|
| date | Mon, 24 Aug 2020 12:14:15 -0400 |
| parents | cd6da887a5f4 |
| children |
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--- a/bundle_collection.xml Fri Aug 04 12:04:09 2017 -0400 +++ b/bundle_collection.xml Mon Aug 24 12:14:15 2020 -0400 @@ -1,71 +1,112 @@ -<tool id="bundle_collection" name="Bundle Collection" version="1.2.1"> - <description>Download a collection of files</description> - <stdio> - <exit_code range="1:" level="fatal" description="Unknown error has occurred"/> - </stdio> - <command interpreter="perl">bundle_collection.pl -h $html_file -p $html_file.files_path +<tool id="bundle_collection" name="Bundle Collection" version="1.3.0"> + <description>Package up and download a collection of files as a single archive.</description> + <requirements> + <requirement type="package" version="2.50">perl-getopt-long</requirement> + <requirement type="package" version="1.69">perl-pod-usage</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + perl '$__tool_directory__/bundle_collection.pl' -h '$html_file' -p '$html_file.files_path' + + #if $singles_or_list.type == "list": - #if $singles_or_list.type == "list": + #if $singles_or_list.input: + #for $f in $singles_or_list.input.keys + -i "$f,$singles_or_list.input[$f].ext=$singles_or_list.input[$f]" + #if $singles_or_list.input[$f].metadata.bam_index and $singles_or_list.input[$f].metadata.bam_index != "None" + #set $bamind = $f+","+$singles_or_list.input[$f].ext+".bai="+$singles_or_list.input[$f].metadata.bam_index + -i "$bamind" + #end if + #end for + #end if + #elif $singles_or_list.type == "singles": + #for $dataset in $singles_or_list.single_files + #if $dataset.single_file: + -i "$dataset.single_file.name,$dataset.single_file.ext=$dataset.single_file" + #end if - #if $singles_or_list.input: - #for $f in $singles_or_list.input.keys - -i "$f,$singles_or_list.input[$f].ext=$singles_or_list.input[$f]" - #if $singles_or_list.input[$f].metadata.bam_index and $singles_or_list.input[$f].metadata.bam_index != "None" - #set $bamind = $f+","+$singles_or_list.input[$f].ext+".bai="+$singles_or_list.input[$f].metadata.bam_index - -i "$bamind" - #end if - #end for - #end if - #elif $singles_or_list.type == "singles": - #for $dataset in $singles_or_list.single_files - #if $dataset.single_file: - -i "$dataset.single_file.name,$dataset.single_file.ext=$dataset.single_file" - #end if + #if $dataset.single_file.metadata.bam_index and $dataset.single_file.metadata.bam_index != "None" + #set $bamind = $dataset.single_file.name+","+$dataset.single_file.ext+".bai="+$dataset.single_file.metadata.bam_index + -i "$bamind" + #end if + #end for + #end if + ]]></command> - #if $dataset.single_file.metadata.bam_index and $dataset.single_file.metadata.bam_index != "None" - #set $bamind = $dataset.single_file.name+","+$dataset.single_file.ext+".bai="+$dataset.single_file.metadata.bam_index - -i "$bamind" - #end if - - #end for - #end if - </command> + <inputs> + <conditional name="singles_or_list"> + <param name="type" type="select" label="Bundle type"> + <option value="singles">Individual datasets</option> + <option value="list">List Collection </option> + </param> + <when value="singles"> + <repeat name='single_files' title='Single dataset(s)'> + <param name="single_file" label="Dataset to add the bundle" type="data" format='data' optional='False'/> + </repeat> + </when> + <when value="list"> + <param name="input" type="data_collection" label="Data Collection" collection_type="list" optional='False'/> + </when> + </conditional> + </inputs> + + <outputs> + <data name="html_file" format="html" label="Bundled Collection" /> + </outputs> - <inputs> - <conditional name="singles_or_list"> - <param name="type" type="select" label="Bundle type"> - <option value="singles">Individual datasets</option> - <option value="list">List Collection </option> - </param> - <when value="singles"> - <repeat name='single_files' title='Single dataset(s)'> - <param name="single_file" label="Dataset to add the bundle" type="data" format='data' optional='False'/> - </repeat> - </when> - <when value="list"> - <param name="input" type="data_collection" label="Data Collection" collection_type="list" optional='False'/> - </when> - </conditional> - </inputs> + <tests> + <test> + <conditional name="singles_or_list"> + <param name="type" value="singles" /> + <repeat name="single_files"> + <param name="single_file" value="first.txt" /> + </repeat> + </conditional> + <output name="html_file" file="out-1.html" /> + </test> + <test> + <conditional name="singles_or_list"> + <param name="type" value="singles" /> + <repeat name="single_files"> + <param name="single_file" value="first.txt" /> + </repeat> + <repeat name="single_files"> + <param name="single_file" value="second.txt" /> + </repeat> + </conditional> + <output name="html_file" file="out-2.html" /> + </test> + <test> + <conditional name="singles_or_list"> + <param name="type" value="list" /> + <param name="input"> + <collection type="list"> + <element name="first.txt" value="first.txt"/> + <element name="second.txt" value="second.txt"/> + </collection> + </param> + </conditional> + <output name="html_file" file="out-2.html" /> + </test> + </tests> - <outputs> - <data name="html_file" format="html" label="Bundled Collection" /> - </outputs> - <tests> - <test> - <output/> - </test> - </tests> + <help><![CDATA[ + ***What it does** + + This tool will bundle up files in a list collection into a downloadable zip file + + Author: Mariam Iskander, Jen Cabral, and Aaron Petkau (Public Health Agency of Canada). + ]]> + </help> - <help> - ***What it does** - - This tool will bundle up files in a list collection into a downloadable zip file - - Author: Mariam Iskander and Jen Cabral - </help> - - <citations> + <citations> + <citation type="bibtex"> + @UNPUBLISHED{PHAC2020, + author = "Public Health Agency of Canada", + title = "Bundle Collections", + year = "2020", + url = {https://github.com/phac-nml/galaxy_tools} + } + </citation> </citations> </tool>