| Previous changeset 2:f84a33bc5c3e (2017-10-14) Next changeset 4:40232a4e5a04 (2017-10-14) |
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Commit message:
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 2a0c81f39a2d50819a327cb889f336b136612d60 |
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modified:
porechop.xml |
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added:
porechop_summarize.pl |
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removed:
f33.fa |
| b |
| diff -r f84a33bc5c3e -r 80408ff0c1f5 f33.fa --- a/f33.fa Sat Oct 14 10:52:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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 |
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| diff -r f84a33bc5c3e -r 80408ff0c1f5 porechop.xml --- a/porechop.xml Sat Oct 14 10:52:30 2017 -0400 +++ b/porechop.xml Sat Oct 14 22:23:22 2017 -0400 |
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| @@ -78,6 +78,9 @@ #end if + | perl $__tool_directory__/porechop_summarize.pl + > $result_table + ]]> </command> @@ -139,11 +142,6 @@ <outputs> - <collection type="list" name="output"> - <discover_datasets pattern="(?P<name>.*)" directory="out" format="fastqsanger" /> - </collection> - - <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string}"> <filter>out_format == 'fastq'</filter> <discover_datasets pattern="(?P<name>.*)" directory="out" format="fastqsanger" /> @@ -153,6 +151,7 @@ <discover_datasets pattern="(?P<name>.*)" directory="out" format="fasta" /> </collection> + <data format="table" name="result_table" label="${tool.name} on ${on_string} (summary)" /> </outputs> <!-- ***************************************************************** --> |
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| diff -r f84a33bc5c3e -r 80408ff0c1f5 porechop_summarize.pl --- /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; + |