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comparison xpore_diffmod.xml @ 1:ff53cf0d0bbd draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
author artbio
date Fri, 28 May 2021 23:32:25 +0000
parents b64b9a2bf4f0
children a5758bb680c8
comparison
equal deleted inserted replaced
0:b64b9a2bf4f0 1:ff53cf0d0bbd
1 <tool id="xpore_diffmod" name="xpore-diffmod" version="0.5.6+galaxy1"> 1 <tool id="xpore_diffmod" name="xpore-diffmod" version="0.5.6+galaxy2">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.5.6">xpore</requirement> 4 <requirement type="package" version="0.5.6">xpore</requirement>
5 <requirement type="package" version="1.9.0">pyensembl</requirement>
6 </requirements> 5 </requirements>
7 <stdio> 6 <stdio>
8 <exit_code range="1:" level="fatal" description="Tool exception" /> 7 <exit_code range="1:" level="fatal" description="Tool exception" />
9 </stdio> 8 </stdio>
10 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
29 printf "\nout: ./out\n" >> config.yml && 28 printf "\nout: ./out\n" >> config.yml &&
30 printf "\nmethod:\n" >> config.yml && 29 printf "\nmethod:\n" >> config.yml &&
31 printf " prefiltering:\n" >> config.yml && 30 printf " prefiltering:\n" >> config.yml &&
32 printf " method: t-test\n" >> config.yml && 31 printf " method: t-test\n" >> config.yml &&
33 printf " threshold: 0.1\n" >> config.yml && 32 printf " threshold: 0.1\n" >> config.yml &&
34
35 xpore-diffmod --config config.yml --n_processes \${GALAXY_SLOTS:-4} && 33 xpore-diffmod --config config.yml --n_processes \${GALAXY_SLOTS:-4} &&
36 sed -i "s/,/\t/g" ./out/diffmod.table 34 sed -i "s/,/\t/g" ./out/diffmod.table &&
35 mv ./out/diffmod.table $diffmod_table &&
36 mv ./out/diffmod.log $diffmod_log &&
37 mv ./config.yml $config
37 38
38 ]]></command> 39 ]]></command>
39 <inputs> 40 <inputs>
40 <param name="control_name" type="text" label="Control condition name" 41 <param name="control_name" type="text" label="Control condition name"
41 help="Only letters, digits and _ will be retained in this field"> 42 help="Only letters, digits and _ will be retained in this field">
62 </repeat> 63 </repeat>
63 64
64 </inputs> 65 </inputs>
65 66
66 <outputs> 67 <outputs>
67 <data format="tabular" name="diffmod_table" label="diffmod table" from_work_dir="./out/diffmod.table" /> 68 <data format="tabular" name="diffmod_table" label="diffmod table" />
68 <data format="txt" name="diffmod_log" label="diffmod log" from_work_dir="./out/diffmod.log" /> 69 <data format="txt" name="diffmod_log" label="diffmod log" />
69 <data format="txt" name="config" label="configuration.yml" from_work_dir="./config.yml" /> 70 <data format="txt" name="config" label="configuration.yml" />
70 </outputs> 71 </outputs>
71 <tests> 72 <tests>
72 <test> 73 <test>
73 <param name="control_name" value="control" /> 74 <param name="control_name" value="control" />
74 <repeat name="ControlReplicates"> 75 <repeat name="ControlReplicates">