| Previous changeset 1:cd6da887a5f4 (2017-08-04) |
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Commit message:
"planemo upload commit 7761f1e59039279728185e751f1a51b56fe14cb0" |
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modified:
bundle_collection.pl bundle_collection.xml |
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added:
test-data/first.txt test-data/out-1.html test-data/out-2.html test-data/second.txt |
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| diff -r cd6da887a5f4 -r 705ebd286b57 bundle_collection.pl --- a/bundle_collection.pl Fri Aug 04 12:04:09 2017 -0400 +++ b/bundle_collection.pl Mon Aug 24 12:14:15 2020 -0400 |
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| @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl use strict; use warnings; @@ -52,57 +52,60 @@ printf $out "<!DOCTYPE html> <html> -<style type=\"text/css\"> - -body { - font-family: sans-serif; - color: #000; - } +<head> + <style type=\"text/css\"> + + body { + font-family: sans-serif; + color: #000; + } + + table { + margin-left: 3em; + text-align: center; + } + th { + text-align:center; + background-color: #000080; + color: #FFF; + padding: 0.4em; + } + td { + font-family: monospace; + text-align: left; + background-color: #EEE; + color: #000; + padding: 0.4em; + } + h2 { + color: #800000; + padding-bottom: 0; + margin-bottom: 0; + clear: left; + } + </style> +</head> -table { - margin-left: 3em; - text-align: center; - } -th { - text-align:center; - background-color: #000080; - color: #FFF; - padding: 0.4em; - } -td { - font-family: monospace; - text-align: left; - background-color: #EEE; - color: #000; - padding: 0.4em; - } -h2 { - color: #800000; - padding-bottom: 0; - margin-bottom: 0; - clear: left; - } -</style></head> +<body> + + <h2 id=\"M0\">Bundle Collection Summary</h2><br><br> - <body> - -<h2 id=\"M0\">Bundle Collection Summary</h2><br><br> + Number of keys: $num_keys<br> + Number of values: $num_vals<br><br> -Number of keys: $num_keys<br> -Number of values: $num_vals<br><br> - -<table border=\"1\"><tr><th>File name</th><th>File type</th></tr>"; + <table border=\"1\"> + <tr><th>File name</th><th>File type</th></tr>\n"; foreach my $key (sort(keys %information)) { foreach my $val (keys %{$information{$key}} ) { - printf $out "<tr><td>$key</td><td>$val</td></tr>"; + printf $out " <tr><td>$key</td><td>$val</td></tr>\n"; } } -printf $out "</table></body></html>"; +printf $out " </table>\n</body>\n</html>"; close $out; @@ -114,7 +117,7 @@ =head1 SYNOPSIS - bundle_collection.pl -h html_file -p output_path -o "key=value" + bundle_collection.pl -h html_file -p output_path -i "key=value" =back -=cut \ No newline at end of file +=cut |
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| diff -r cd6da887a5f4 -r 705ebd286b57 bundle_collection.xml --- a/bundle_collection.xml Fri Aug 04 12:04:09 2017 -0400 +++ b/bundle_collection.xml Mon Aug 24 12:14:15 2020 -0400 |
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| @@ -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> |
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| diff -r cd6da887a5f4 -r 705ebd286b57 test-data/first.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/first.txt Mon Aug 24 12:14:15 2020 -0400 |
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| @@ -0,0 +1,1 @@ +first |
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| diff -r cd6da887a5f4 -r 705ebd286b57 test-data/out-1.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out-1.html Mon Aug 24 12:14:15 2020 -0400 |
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| @@ -0,0 +1,49 @@ +<!DOCTYPE html> +<html> +<head> + <style type="text/css"> + + body { + font-family: sans-serif; + color: #000; + } + + table { + margin-left: 3em; + text-align: center; + } + th { + text-align:center; + background-color: #000080; + color: #FFF; + padding: 0.4em; + } + td { + font-family: monospace; + text-align: left; + background-color: #EEE; + color: #000; + padding: 0.4em; + } + h2 { + color: #800000; + padding-bottom: 0; + margin-bottom: 0; + clear: left; + } + </style> +</head> + +<body> + + <h2 id="M0">Bundle Collection Summary</h2><br><br> + + Number of keys: 1<br> + Number of values: 1<br><br> + + <table border="1"> + <tr><th>File name</th><th>File type</th></tr> + <tr><td>first.txt</td><td>txt</td></tr> + </table> +</body> +</html> \ No newline at end of file |
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| diff -r cd6da887a5f4 -r 705ebd286b57 test-data/out-2.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out-2.html Mon Aug 24 12:14:15 2020 -0400 |
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| @@ -0,0 +1,50 @@ +<!DOCTYPE html> +<html> +<head> + <style type="text/css"> + + body { + font-family: sans-serif; + color: #000; + } + + table { + margin-left: 3em; + text-align: center; + } + th { + text-align:center; + background-color: #000080; + color: #FFF; + padding: 0.4em; + } + td { + font-family: monospace; + text-align: left; + background-color: #EEE; + color: #000; + padding: 0.4em; + } + h2 { + color: #800000; + padding-bottom: 0; + margin-bottom: 0; + clear: left; + } + </style> +</head> + +<body> + + <h2 id="M0">Bundle Collection Summary</h2><br><br> + + Number of keys: 2<br> + Number of values: 2<br><br> + + <table border="1"> + <tr><th>File name</th><th>File type</th></tr> + <tr><td>first.txt</td><td>txt</td></tr> + <tr><td>second.txt</td><td>txt</td></tr> + </table> +</body> +</html> \ No newline at end of file |
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| diff -r cd6da887a5f4 -r 705ebd286b57 test-data/second.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/second.txt Mon Aug 24 12:14:15 2020 -0400 |
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| @@ -0,0 +1,1 @@ +second |