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comparison bellerophon.xml @ 0:eca6296a091a draft

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"planemo upload for repository https://github.com/davebx/bellerophon commit 5fe46c36adac4843cd548802073aa62b0afc61cd"
author iuc
date Fri, 28 May 2021 20:54:47 +0000
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children 25ca5d73aedf
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-1:000000000000 0:eca6296a091a
1 <tool id="bellerophon" name="Filter and merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>chimeric reads from Arima Genomics</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.0</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">bellerophon</requirement>
9 <requirement type="package" version="1.12">samtools</requirement>
10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[
12 #if $forward.is_of_type("sam"):
13 #set $forward_input = 'forward_input.sam'
14 ln -s '${forward}' '$forward_input' &&
15 #else:
16 #set $forward_input = 'forward_input.bam'
17 ln -s '${forward}' '$forward_input' &&
18 #end if
19 #if $reverse.is_of_type("sam"):
20 #set $reverse_input = 'reverse_input.sam'
21 ln -s '${reverse}' '$reverse_input' &&
22 #else:
23 #set $reverse_input = 'reverse_input.bam'
24 ln -s '${reverse}' '$reverse_input' &&
25 #end if
26 bellerophon
27 --forward $forward_input
28 --reverse $reverse_input
29 --quality $quality
30 --output 'merged_out.bam'
31 && samtools sort --no-PG -O BAM -o '$outfile' -@ \${GALAXY_SLOTS:-1} merged_out.bam
32 ]]>
33 </command>
34 <inputs>
35 <param argument="--forward" type="data" format="qname_sorted.bam,sam" label="First set of reads"
36 help="This is usually the forward reads in your experiment." />
37 <param argument="--reverse" type="data" format="qname_sorted.bam,sam" label="Second set of reads"
38 help="This is usually the reverse reads in your experiment." />
39 <param argument="--quality" type="integer" value="20" label="Minimum mapping quality"/>
40 </inputs>
41 <outputs>
42 <data name="outfile" format="bam"/>
43 </outputs>
44 <tests>
45 <test expect_num_outputs="1">
46 <param name="forward" value="forward.bam" ftype="qname_sorted.bam" />
47 <param name="reverse" value="reverse.bam" ftype="qname_sorted.bam" />
48 <param name="quality" value="20" />
49 <output name="outfile" file="merged-out.bam" ftype="bam" />
50 </test>
51 <test expect_num_outputs="1">
52 <param name="forward" value="forward.sam" ftype="sam" />
53 <param name="reverse" value="reverse.sam" ftype="sam" />
54 <param name="quality" value="12" />
55 <output name="outfile" file="merged-sam.bam" ftype="bam" />
56 </test>
57 </tests>
58 <help><![CDATA[
59 Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. This is usually needed when dealing with data from Arima Genomics.
60 ]]></help>
61 <citations>
62 <citation type="doi">10.1038/s41586-021-03451-0</citation>
63 </citations>
64 </tool>