Mercurial > repos > nml > bundle_collections

changeset 2:705ebd286b57 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 7761f1e59039279728185e751f1a51b56fe14cb0"
author nml
date Mon, 24 Aug 2020 12:14:15 -0400
parents cd6da887a5f4
children
files bundle_collection.pl bundle_collection.xml test-data/first.txt test-data/out-1.html test-data/out-2.html test-data/second.txt
diffstat 6 files changed, 249 insertions(+), 104 deletions(-) [+]
line wrap: on
line diff
--- a/bundle_collection.pl	Fri Aug 04 12:04:09 2017 -0400
+++ b/bundle_collection.pl	Mon Aug 24 12:14:15 2020 -0400
@@ -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
--- 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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/first.txt	Mon Aug 24 12:14:15 2020 -0400
@@ -0,0 +1,1 @@
+first
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out-1.html	Mon Aug 24 12:14:15 2020 -0400
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out-2.html	Mon Aug 24 12:14:15 2020 -0400
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/second.txt	Mon Aug 24 12:14:15 2020 -0400
@@ -0,0 +1,1 @@
+second