| Previous changeset 0:bae199dc511f (2015-11-20) Next changeset 2:705ebd286b57 (2020-08-24) |
|
Commit message:
planemo upload commit 44ee87b603c444f0ae5f73dea57d4ed2f589a4eb |
|
modified:
bundle_collection.xml |
| b |
| diff -r bae199dc511f -r cd6da887a5f4 bundle_collection.xml --- a/bundle_collection.xml Fri Nov 20 10:23:17 2015 -0500 +++ b/bundle_collection.xml Fri Aug 04 12:04:09 2017 -0400 |
| [ |
| @@ -1,28 +1,71 @@ -<tool id="bundle_collection" name="Bundle Collection" version="1.0.1"> +<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 - #for $f in $input.keys - -i "$f,$input[$f].ext=$input[$f]" - #if $input[$f].metadata.bam_index and $input[$f].metadata.bam_index != "None" - #set $bamind = $f+","+$input[$f].ext+".bai="+$input[$f].metadata.bam_index - -i "$bamind" - #end if - #end for + + #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 $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> - <param name="input" type="data_collection" label="Data Collection" collection_type="list"/> + <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> + <tests> + <test> + <output/> + </test> + </tests> + <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> + </tool> |