Mercurial > repos > artbio > xpore

annotate xpore_diffmod.xml @ 0:b64b9a2bf4f0 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
author artbio
date Wed, 26 May 2021 23:14:24 +0000
parents
children ff53cf0d0bbd
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b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
1 <tool id="xpore_diffmod" name="xpore-diffmod" version="0.5.6+galaxy1">
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
2 <description></description>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
3 <requirements>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
4 <requirement type="package" version="0.5.6">xpore</requirement>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
5 <requirement type="package" version="1.9.0">pyensembl</requirement>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
6 </requirements>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
7 <stdio>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
8 <exit_code range="1:" level="fatal" description="Tool exception" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
9 </stdio>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
10 <command detect_errors="exit_code"><![CDATA[
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
11 printf "notes: Pairwise comparison without replicates with default parameter setting.\n\n" >> config.yml &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
12 printf "data:\n" >> config.yml &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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13 printf " ${control_name}:\n" >> config.yml &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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14 #for $i, $s in enumerate($ControlReplicates):
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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15 printf " rep${i}: ./${control_name}_${i}\n" >> config.yml &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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16 mkdir ${control_name}_${i} &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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17 ln -s ${s.ControlJson} ${control_name}_${i}/data.json &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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18 ln -s ${s.ControlIndex} ${control_name}_${i}/data.index &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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19 ln -s ${s.ControlReadcount} ${control_name}_${i}/data.readcount &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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20 #end for
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
21 printf " ${test_name}:\n" >> config.yml &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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22 #for $i, $s in enumerate($TestReplicates):
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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23 printf " rep${i}: ./${test_name}_${i}\n" >> config.yml &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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24 mkdir ${test_name}_${i} &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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25 ln -s ${s.TestJson} ${test_name}_${i}/data.json &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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26 ln -s ${s.TestIndex} ${test_name}_${i}/data.index &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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27 ln -s ${s.TestReadcount} ${test_name}_${i}/data.readcount &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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28 #end for
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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29 printf "\nout: ./out\n" >> config.yml &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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30 printf "\nmethod:\n" >> config.yml &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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31 printf " prefiltering:\n" >> config.yml &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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32 printf " method: t-test\n" >> config.yml &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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33 printf " threshold: 0.1\n" >> config.yml &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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34
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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35 xpore-diffmod --config config.yml --n_processes \${GALAXY_SLOTS:-4} &&
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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36 sed -i "s/,/\t/g" ./out/diffmod.table
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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37
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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38 ]]></command>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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39 <inputs>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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40 <param name="control_name" type="text" label="Control condition name"
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
41 help="Only letters, digits and _ will be retained in this field">
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
42 <sanitizer>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
43 <valid initial="string.letters,string.digits"><add value="_" /></valid>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
44 </sanitizer>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
45 </param>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
46 <repeat name="ControlReplicates" title="Control replicates" min="1">
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
47 <param name="ControlJson" label="json from xpore-dataprep" type="data" format="json" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
48 <param name="ControlIndex" label="index from xpore-dataprep" type="data" format="txt" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
49 <param name="ControlReadcount" label="Readcount from xpore-dataprep" type="data" format="txt" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
50 </repeat>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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51
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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52 <param name="test_name" type="text" label="Test condition name"
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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53 help="Only letters, digits and _ will be retained in this field">
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
54 <sanitizer>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
55 <valid initial="string.letters,string.digits"><add value="_" /></valid>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
56 </sanitizer>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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57 </param>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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58 <repeat name="TestReplicates" title="Test replicates" min="1">
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
59 <param name="TestJson" label="json from xpore-dataprep" type="data" format="json" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
60 <param name="TestIndex" label="index from xpore-dataprep" type="data" format="txt" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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61 <param name="TestReadcount" label="Readcount from xpore-dataprep" type="data" format="txt" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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62 </repeat>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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63
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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64 </inputs>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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65
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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66 <outputs>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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67 <data format="tabular" name="diffmod_table" label="diffmod table" from_work_dir="./out/diffmod.table" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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68 <data format="txt" name="diffmod_log" label="diffmod log" from_work_dir="./out/diffmod.log" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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69 <data format="txt" name="config" label="configuration.yml" from_work_dir="./config.yml" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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70 </outputs>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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71 <tests>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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72 <test>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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73 <param name="control_name" value="control" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
74 <repeat name="ControlReplicates">
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
75 <param name="ControlJson" value="inputs_xpore-diffmod/C1_data.json" ftype="json" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
76 <param name="ControlIndex" value="inputs_xpore-diffmod/C1_data.index" ftype="txt" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
77 <param name="ControlReadcount" value="inputs_xpore-diffmod/C1_data.readcount" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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78 </repeat>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
parents:
diff changeset
79 <repeat name="ControlReplicates">
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
80 <param name="ControlJson" value="inputs_xpore-diffmod/C2_data.json" ftype="json" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
81 <param name="ControlIndex" value="inputs_xpore-diffmod/C2_data.index" ftype="txt" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
82 <param name="ControlReadcount" value="inputs_xpore-diffmod/C2_data.readcount" ftype="txt" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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diff changeset
83 </repeat>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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84 <param name="test_name" value="test" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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85 <repeat name="TestReplicates">
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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86 <param name="TestJson" value="inputs_xpore-diffmod/T1_data.json" ftype="json"/>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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87 <param name="TestIndex" value="inputs_xpore-diffmod/T1_data.index" ftype="txt" />
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88 <param name="TestReadcount" value="inputs_xpore-diffmod/T1_data.readcount" ftype="txt" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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89 </repeat>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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90 <repeat name="TestReplicates">
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91 <param name="TestJson" value="inputs_xpore-diffmod/T2_data.json" ftype="json"/>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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92 <param name="TestIndex" value="inputs_xpore-diffmod/T2_data.index" ftype="txt" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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93 <param name="TestReadcount" value="inputs_xpore-diffmod/T2_data.readcount" ftype="txt" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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94 </repeat>
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95 <output file="diffmod.table" name="diffmod_table" ftype="tabular" compare="sim_size" delta="400" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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96 <output file="diffmod.log" name="diffmod_log" ftype="txt" />
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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97 </test>
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98 </tests>
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99 <help>
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100
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101 **What it does**
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102
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103 This tool is a basic wrapper of xpore-diffmod for analysis of differential RNA modification
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104 across all tested positions.
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105
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106 .. class:: warningmark
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107
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108 In its current version, only the analysis based on a transcripts collection reference is
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109 implemented.
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110
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111 **Inputs**
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112
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113 You need 3 input datasets generated by the tool xpore-dataprep::
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114
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115 - data.index
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116 - data.json
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117 - data.readcount
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118
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119
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120 **Output**
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121
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122 - a diffmod_table of the differential RNA modifications across all tested positions of transcripts
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123 - a diffmod.log of the analysis
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124
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125 for details on xpore-diffmod, see https://xpore.readthedocs.io/en/latest/index.html
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126 and https://github.com/GoekeLab/xpore
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127
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128
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129 </help>
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130
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131 <citations>
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132 <citation type="doi">10.1101/2020.06.18.160010</citation>
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133 </citations>
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134 </tool>