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comparison dexseq_count.xml @ 17:d104044e4257 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
author iuc
date Tue, 04 Apr 2023 08:25:36 +0000
parents 781f60a0c658
children ffa256d657b2
comparison
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16:661f29c77bb0 17:d104044e4257
1 <tool id="dexseq_count" name="DEXSeq-Count" version="@TOOL_VERSION@.1" profile="@PROFILE@"> 1 <tool id="dexseq_count" name="DEXSeq-Count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Prepare and count exon abundancies from RNA-seq data</description> 2 <description>Prepare and count exon abundancies from RNA-seq data</description>
3 <xrefs>
4 <xref type="bio.tools">dexseq</xref>
5 </xrefs>
6 <macros> 3 <macros>
7 <import>macros.xml</import> 4 <import>macros.xml</import>
8 </macros> 5 </macros>
9 <expand macro="requirements"> 6 <expand macro="xrefs"/>
10 </expand> 7 <expand macro="requirements"/>
11 <stdio> 8 <stdio>
12 <!-- Anything other than zero is an error --> 9 <!-- Anything other than zero is an error -->
13 <exit_code range="1:" /> 10 <exit_code range="1:" />
14 <exit_code range=":-1" /> 11 <exit_code range=":-1" />
15 <!-- In case the return code has not been set propery check stderr too --> 12 <!-- In case the return code has not been set propery check stderr too -->
30 --minaqual $mode.qual 27 --minaqual $mode.qual
31 --order $mode.order 28 --order $mode.order
32 $mode.flattened_gtf_in 29 $mode.flattened_gtf_in
33 '$mode.bamfile' 30 '$mode.bamfile'
34 '$counts_file' 31 '$counts_file'
32 &&
33 sed -i 's/\"//g' '$counts_file'
35 #end if 34 #end if
36 ]]></command> 35 ]]></command>
37 <inputs> 36 <inputs>
38 <conditional name="mode"> 37 <conditional name="mode">
39 <param name="mode_select" type="select" label="Mode of operation"> 38 <param name="mode_select" type="select" label="Mode of operation">