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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 59e86ba957774b2fb86b3f5dbd7be24f99dd60f7
author artbio
date Sun, 15 May 2022 15:11:49 +0000
parents ff53cf0d0bbd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2
a5758bb680c8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 59e86ba957774b2fb86b3f5dbd7be24f99dd60f7
artbio
parents: 1
diff changeset
1 <tool id="xpore_diffmod" name="xpore-diffmod" version="2.1+galaxy0">
0
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>
2
a5758bb680c8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 59e86ba957774b2fb86b3f5dbd7be24f99dd60f7
artbio
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4 <requirement type="package" version="2.1">xpore</requirement>
0
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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5 </requirements>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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6 <stdio>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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7 <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
8 </stdio>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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9 <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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10 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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11 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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12 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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13 #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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14 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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15 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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16 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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17 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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18 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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19 #end for
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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20 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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21 #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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22 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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23 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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24 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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25 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"
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26 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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27 #end for
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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28 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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29 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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30 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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31 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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32 printf " threshold: 0.1\n" >> config.yml &&
2
a5758bb680c8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 59e86ba957774b2fb86b3f5dbd7be24f99dd60f7
artbio
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33 xpore diffmod --config config.yml --n_processes \${GALAXY_SLOTS:-4} &&
1
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
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34 sed -i "s/,/\t/g" ./out/diffmod.table &&
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
artbio
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35 mv ./out/diffmod.table $diffmod_table &&
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
artbio
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36 mv ./out/diffmod.log $diffmod_log &&
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
artbio
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37 mv ./config.yml $config
0
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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38
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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39 ]]></command>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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40 <inputs>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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41 <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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42 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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43 <sanitizer>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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44 <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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45 </sanitizer>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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46 </param>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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47 <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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48 <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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49 <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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50 <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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51 </repeat>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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52
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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53 <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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54 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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55 <sanitizer>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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56 <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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57 </sanitizer>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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58 </param>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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59 <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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60 <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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61 <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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62 <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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63 </repeat>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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64
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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65 </inputs>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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66
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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67 <outputs>
1
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
artbio
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68 <data format="tabular" name="diffmod_table" label="diffmod table" />
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
artbio
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69 <data format="txt" name="diffmod_log" label="diffmod log" />
ff53cf0d0bbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
artbio
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70 <data format="txt" name="config" label="configuration.yml" />
0
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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71 </outputs>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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72 <tests>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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73 <test>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
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74 <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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75 <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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76 <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
77 <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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78 <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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79 </repeat>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
artbio
parents:
diff changeset
80 <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
81 <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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82 <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
83 <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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84 </repeat>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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85 <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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86 <repeat name="TestReplicates">
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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87 <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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88 <param name="TestIndex" value="inputs_xpore-diffmod/T1_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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89 <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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90 </repeat>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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91 <repeat name="TestReplicates">
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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92 <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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93 <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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94 <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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95 </repeat>
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.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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97 <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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98 </test>
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99 </tests>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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100 <help>
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101
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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102 **What it does**
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103
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104 This tool is a basic wrapper of xpore-diffmod for analysis of differential RNA modification
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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105 across all tested positions.
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106
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107 .. class:: warningmark
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108
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109 In its current version, only the analysis based on a transcripts collection reference is
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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110 implemented.
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111
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112 **Inputs**
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113
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114 You need 3 input datasets generated by the tool xpore-dataprep::
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115
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116 - data.index
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117 - data.json
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118 - data.readcount
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119
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120
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121 **Output**
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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122
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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123 - a diffmod_table of the differential RNA modifications across all tested positions of transcripts
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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124 - a diffmod.log of the analysis
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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125
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126 for details on xpore-diffmod, see https://xpore.readthedocs.io/en/latest/index.html
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127 and https://github.com/GoekeLab/xpore
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128
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129
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130 </help>
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131
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132 <citations>
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133 <citation type="doi">10.1101/2020.06.18.160010</citation>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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134 </citations>
b64b9a2bf4f0 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
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135 </tool>