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comparison bam2wig.xml @ 34:8fbd165f8835

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Patch from Bjorn Gruning
author lparsons
date Mon, 04 Nov 2013 16:19:36 -0500
parents 580ee0c4bc4e
children
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33:073c77ce5e94 34:8fbd165f8835
6 <requirement type="package" version="3.0.1">R</requirement> 6 <requirement type="package" version="3.0.1">R</requirement>
7 <requirement type="package" version="1.7.1">numpy</requirement> 7 <requirement type="package" version="1.7.1">numpy</requirement>
8 <requirement type="package" version="2.3.7">rseqc</requirement> 8 <requirement type="package" version="2.3.7">rseqc</requirement>
9 </requirements> 9 </requirements>
10 <command> 10 <command>
11 tmp_input_name=\$(mktemp -u);
12 bai='.bai';
11 13
12 #import tempfile, os 14 ln -s "${input}" \$tmp_input_name &amp;&amp;
13 #set $tmp_input = tempfile.NamedTemporaryFile() 15 ln -s "${input.metadata.bam_index}" \$tmp_input_name\$bai &amp;&amp;
14 #set $tmp_input_name = $input_singles_tmp_handle.name 16 bam2wig.py -i \$tmp_input_name -s $chromsize -o outfile
15 #silent $tmp_input.close()
16
17 ln -s "${input}" $tmp_input_name &amp;&amp;
18 ln -s "${input.metadata.bam_index}" $tmp_input_name + ".bai" &amp;&amp;
19 bam2wig.py -i "local_input.bam" -s $chromsize -o outfile
20 17
21 #if str($strand_type.strand_specific) == "pair" 18 #if str($strand_type.strand_specific) == "pair"
22 -d 19 -d
23 #if str($strand_type.pair_type) == "sd" 20 #if str($strand_type.pair_type) == "sd"
24 '1++,1--,2+-,2-+' 21 '1++,1--,2+-,2-+'
42 39
43 #if $skipmultihits 40 #if $skipmultihits
44 -u 41 -u
45 #end if 42 #end if
46 ; 43 ;
47 rm $tmp_input_name + ".bai" ; 44 rm "\$tmp_input_name\$bai";
48 rm $tmp_input_name 45 rm \$tmp_input_name
49 </command> 46 </command>
50 <inputs> 47 <inputs>
51 <param name="input" type="data" label="Input .bam File" format="bam" /> 48 <param name="input" type="data" label="Input .bam File" format="bam" />
52 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" /> 49 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" />
53 <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" /> 50 <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" />