Mercurial > repos > nml > bundle_collections
comparison 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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| 1:cd6da887a5f4 | 2:705ebd286b57 |
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| 1 <tool id="bundle_collection" name="Bundle Collection" version="1.2.1"> | 1 <tool id="bundle_collection" name="Bundle Collection" version="1.3.0"> |
| 2 <description>Download a collection of files</description> | 2 <description>Package up and download a collection of files as a single archive.</description> |
| 3 <stdio> | 3 <requirements> |
| 4 <exit_code range="1:" level="fatal" description="Unknown error has occurred"/> | 4 <requirement type="package" version="2.50">perl-getopt-long</requirement> |
| 5 </stdio> | 5 <requirement type="package" version="1.69">perl-pod-usage</requirement> |
| 6 <command interpreter="perl">bundle_collection.pl -h $html_file -p $html_file.files_path | 6 </requirements> |
| 7 <command detect_errors="aggressive"><![CDATA[ | |
| 8 perl '$__tool_directory__/bundle_collection.pl' -h '$html_file' -p '$html_file.files_path' | |
| 7 | 9 |
| 8 #if $singles_or_list.type == "list": | 10 #if $singles_or_list.type == "list": |
| 9 | 11 |
| 10 #if $singles_or_list.input: | 12 #if $singles_or_list.input: |
| 11 #for $f in $singles_or_list.input.keys | 13 #for $f in $singles_or_list.input.keys |
| 12 -i "$f,$singles_or_list.input[$f].ext=$singles_or_list.input[$f]" | 14 -i "$f,$singles_or_list.input[$f].ext=$singles_or_list.input[$f]" |
| 13 #if $singles_or_list.input[$f].metadata.bam_index and $singles_or_list.input[$f].metadata.bam_index != "None" | 15 #if $singles_or_list.input[$f].metadata.bam_index and $singles_or_list.input[$f].metadata.bam_index != "None" |
| 14 #set $bamind = $f+","+$singles_or_list.input[$f].ext+".bai="+$singles_or_list.input[$f].metadata.bam_index | 16 #set $bamind = $f+","+$singles_or_list.input[$f].ext+".bai="+$singles_or_list.input[$f].metadata.bam_index |
| 15 -i "$bamind" | 17 -i "$bamind" |
| 16 #end if | 18 #end if |
| 17 #end for | 19 #end for |
| 18 #end if | 20 #end if |
| 19 #elif $singles_or_list.type == "singles": | 21 #elif $singles_or_list.type == "singles": |
| 20 #for $dataset in $singles_or_list.single_files | 22 #for $dataset in $singles_or_list.single_files |
| 21 #if $dataset.single_file: | 23 #if $dataset.single_file: |
| 22 -i "$dataset.single_file.name,$dataset.single_file.ext=$dataset.single_file" | 24 -i "$dataset.single_file.name,$dataset.single_file.ext=$dataset.single_file" |
| 23 #end if | 25 #end if |
| 24 | 26 |
| 25 #if $dataset.single_file.metadata.bam_index and $dataset.single_file.metadata.bam_index != "None" | 27 #if $dataset.single_file.metadata.bam_index and $dataset.single_file.metadata.bam_index != "None" |
| 26 #set $bamind = $dataset.single_file.name+","+$dataset.single_file.ext+".bai="+$dataset.single_file.metadata.bam_index | 28 #set $bamind = $dataset.single_file.name+","+$dataset.single_file.ext+".bai="+$dataset.single_file.metadata.bam_index |
| 27 -i "$bamind" | 29 -i "$bamind" |
| 28 #end if | 30 #end if |
| 29 | 31 #end for |
| 30 #end for | 32 #end if |
| 31 #end if | 33 ]]></command> |
| 32 </command> | |
| 33 | 34 |
| 34 <inputs> | 35 <inputs> |
| 35 <conditional name="singles_or_list"> | 36 <conditional name="singles_or_list"> |
| 36 <param name="type" type="select" label="Bundle type"> | 37 <param name="type" type="select" label="Bundle type"> |
| 37 <option value="singles">Individual datasets</option> | 38 <option value="singles">Individual datasets</option> |
| 38 <option value="list">List Collection </option> | 39 <option value="list">List Collection </option> |
| 39 </param> | 40 </param> |
| 40 <when value="singles"> | 41 <when value="singles"> |
| 41 <repeat name='single_files' title='Single dataset(s)'> | 42 <repeat name='single_files' title='Single dataset(s)'> |
| 42 <param name="single_file" label="Dataset to add the bundle" type="data" format='data' optional='False'/> | 43 <param name="single_file" label="Dataset to add the bundle" type="data" format='data' optional='False'/> |
| 43 </repeat> | 44 </repeat> |
| 44 </when> | 45 </when> |
| 45 <when value="list"> | 46 <when value="list"> |
| 46 <param name="input" type="data_collection" label="Data Collection" collection_type="list" optional='False'/> | 47 <param name="input" type="data_collection" label="Data Collection" collection_type="list" optional='False'/> |
| 47 </when> | 48 </when> |
| 48 </conditional> | 49 </conditional> |
| 49 </inputs> | 50 </inputs> |
| 50 | 51 |
| 51 <outputs> | 52 <outputs> |
| 52 <data name="html_file" format="html" label="Bundled Collection" /> | 53 <data name="html_file" format="html" label="Bundled Collection" /> |
| 53 </outputs> | 54 </outputs> |
| 54 <tests> | |
| 55 <test> | |
| 56 <output/> | |
| 57 </test> | |
| 58 </tests> | |
| 59 | 55 |
| 60 <help> | 56 <tests> |
| 61 ***What it does** | 57 <test> |
| 58 <conditional name="singles_or_list"> | |
| 59 <param name="type" value="singles" /> | |
| 60 <repeat name="single_files"> | |
| 61 <param name="single_file" value="first.txt" /> | |
| 62 </repeat> | |
| 63 </conditional> | |
| 64 <output name="html_file" file="out-1.html" /> | |
| 65 </test> | |
| 66 <test> | |
| 67 <conditional name="singles_or_list"> | |
| 68 <param name="type" value="singles" /> | |
| 69 <repeat name="single_files"> | |
| 70 <param name="single_file" value="first.txt" /> | |
| 71 </repeat> | |
| 72 <repeat name="single_files"> | |
| 73 <param name="single_file" value="second.txt" /> | |
| 74 </repeat> | |
| 75 </conditional> | |
| 76 <output name="html_file" file="out-2.html" /> | |
| 77 </test> | |
| 78 <test> | |
| 79 <conditional name="singles_or_list"> | |
| 80 <param name="type" value="list" /> | |
| 81 <param name="input"> | |
| 82 <collection type="list"> | |
| 83 <element name="first.txt" value="first.txt"/> | |
| 84 <element name="second.txt" value="second.txt"/> | |
| 85 </collection> | |
| 86 </param> | |
| 87 </conditional> | |
| 88 <output name="html_file" file="out-2.html" /> | |
| 89 </test> | |
| 90 </tests> | |
| 62 | 91 |
| 63 This tool will bundle up files in a list collection into a downloadable zip file | 92 <help><![CDATA[ |
| 93 ***What it does** | |
| 64 | 94 |
| 65 Author: Mariam Iskander and Jen Cabral | 95 This tool will bundle up files in a list collection into a downloadable zip file |
| 66 </help> | |
| 67 | 96 |
| 68 <citations> | 97 Author: Mariam Iskander, Jen Cabral, and Aaron Petkau (Public Health Agency of Canada). |
| 98 ]]> | |
| 99 </help> | |
| 100 | |
| 101 <citations> | |
| 102 <citation type="bibtex"> | |
| 103 @UNPUBLISHED{PHAC2020, | |
| 104 author = "Public Health Agency of Canada", | |
| 105 title = "Bundle Collections", | |
| 106 year = "2020", | |
| 107 url = {https://github.com/phac-nml/galaxy_tools} | |
| 108 } | |
| 109 </citation> | |
| 69 </citations> | 110 </citations> |
| 70 | 111 |
| 71 </tool> | 112 </tool> |