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changeset 3:80408ff0c1f5 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60
author jdv
date Sat, 14 Oct 2017 22:23:22 -0400
parents f84a33bc5c3e
children 40232a4e5a04
files f33.fa porechop.xml porechop_summarize.pl
diffstat 3 files changed, 31 insertions(+), 202 deletions(-) [+]
line wrap: on
line diff
--- a/f33.fa	Sat Oct 14 10:52:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,197 +0,0 @@
->BC01_1st
-GGTGCTG
-AAGAAAGTTGTCGGTGTCTTTGTG
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC02_1st
-GGTGCTG
-TCGATTCCGTTTGTAGTCGTCTGT
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC03_1st
-GGTGCTG
-GAGTCTTGTGTCCCAGTTACCAGG
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC04_1st
-GGTGCTG
-TTCGGATTCTATCGTGTTTCCCTA
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC05_1st
-GGTGCTG
-CTTGTCCAGGGTTTGTGTAACCTT
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC06_1st
-GGTGCTG
-TTCTCGCAAAGGCAGAAAGTAGTC
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC07_1st
-GGTGCTG
-GTGTTACCGTGGGAATGAATCCTT
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC08_1st
-GGTGCTG
-TTCAGGGAACAAACCAAGTTACGT
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC09_1st
-GGTGCTG
-AACTAGGCACAGCGAGTCTTGGTT
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC10_1st
-GGTGCTG
-AAGCGTTGAAACCTTTGTCCTCTC
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC11_1st
-GGTGCTG
-GTTTCATCTATCGGAGGGAATGGA
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC12_1st
-GGTGCTG
-CAGGTAGAAAGAAGCAGAATCGGA
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC13_1st
-GGTGCTG
-AGAACGACTTCCATACTCGTGTGA
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC14_1st
-GGTGCTG
-AACGAGTCTCTTGGGACCCATAGA
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC15_1st
-GGTGCTG
-AGGTCTACCTCGCTAACACCACTG
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC16_1st
-GGTGCTG
-CGTCAACTGACAGTGGTTCGTACT
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC17_1st
-GGTGCTG
-ACCCTCCAGGAAAGTACCTCTGAT
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC18_1st
-GGTGCTG
-CCAAACCCAACAACCTAGATAGGC
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC19_1st
-GGTGCTG
-GTTCCTCGTGCAGTGTCAAGAGAT
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC20_1st
-GGTGCTG
-TTGCGTCCTGTTACGAGAACTCAT
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC21_1st
-GGTGCTG
-GAGCCTCTCATTGTCCGTTCTCTA
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC22_1st
-GGTGCTG
-ACCACTGCCATGTATCAAAGTACG
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC23_1st
-GGTGCTG
-CTTACTACCCAGTGAACCTCCTCG
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC24_1st
-GGTGCTG
-GCATAGTTCTGCATGATGGGTTAG
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC25_1st
-GGTGCTG
-GTAAGTTGGGTATGCAACGCAATG
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC26_1st
-GGTGCTG
-CATACAGCGACTACGCATTCTCAT
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC27_1st
-GGTGCTG
-CGACGGTTAGATTCACCTCTTACA
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC28_1st
-GGTGCTG
-TGAAACCTAAGAAGGCACCGTATC
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC29_1st
-GGTGCTG
-CTAGACACCTTGGGTTGACAGACC
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC30_1st
-GGTGCTG
-TCAGTGAGGATCTACTTCGACCCA
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC31_1st
-GGTGCTG
-TGCGTACAGCAATCAGTTACATTG
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC32_1st
-GGTGCTG
-CCAGTAGAAGTCCGACAACGTCAT
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
-
->BC33_1st
-GGTGCTG
-CAGACTTGGTACGGTTGGGTAACT
-TTAACCT
-TTCTGTTGGTGCTGATATTGC
--- a/porechop.xml	Sat Oct 14 10:52:30 2017 -0400
+++ b/porechop.xml	Sat Oct 14 22:23:22 2017 -0400
@@ -78,6 +78,9 @@
 
         #end if
 
+        | perl $__tool_directory__/porechop_summarize.pl
+        > $result_table
+
     ]]>
     </command>
 
@@ -139,11 +142,6 @@
 
     <outputs>
 
-        <collection type="list" name="output">
-            <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="out" format="fastqsanger" />
-        </collection>
-
-
         <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string}">
             <filter>out_format == 'fastq'</filter>
             <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="out" format="fastqsanger" />
@@ -153,6 +151,7 @@
             <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="out" format="fasta" />
         </collection>
 
+        <data format="table" name="result_table" label="${tool.name} on ${on_string} (summary)" /> 
     </outputs>
 
     <!-- ***************************************************************** -->
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/porechop_summarize.pl	Sat Oct 14 22:23:22 2017 -0400
@@ -0,0 +1,27 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use 5.012;
+
+my $flag = 0;
+my $table;
+
+while (my $line = <STDIN>) {
+
+    print STDERR $line;
+
+    if ($line =~ /Barcode\s+Reads\s+Bases\s+File/) {
+        $flag = 1;
+    }
+    next if (! $flag);
+
+    $table .= $line;
+
+}
+
+$table =~ s/(^\s+|\e\[\d+m)//gms;
+say $table;
+
+exit;
+