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annotate chira_quantify.xml @ 1:34f790d4d085 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 6845f3b028a42acbefb07c5f59fd2e558f50a768"
author iuc
date Mon, 02 Mar 2020 18:33:33 +0000
parents f7cce908ef9f
children 5f9b51cc2b4f
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f7cce908ef9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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1 <tool id="chira_quantify" name="ChiRA qauntify" version="@WRAPPER_VERSION@0">
f7cce908ef9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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2 <description>quantify aligned loci to score the alignments</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command><![CDATA[
f7cce908ef9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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8 chira_quantify.py
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9 -b '$segments'
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10 -m '$merged'
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11 -cs '$crl_share'
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12 -ls '$min_locus_size'
f7cce908ef9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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13 -e '$em_threshold'
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34f790d4d085 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 6845f3b028a42acbefb07c5f59fd2e558f50a768"
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14 $crl
0
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15 -o ./
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16 ]]></command>
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17
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18 <inputs>
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19 <param format="bed" name="segments" type="data" label="BED file of aligned segments"/>
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20 <param format="tabular" name="merged" type="data" label="Tabular file of merged alignments"/>
f7cce908ef9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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21 <param name="crl_share" type="float" value="0.7" label="CRL locus fraction" min="0" max="1"
f7cce908ef9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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22 help="Minimum fraction of reads of a locus that must overlap with all CRL loci inorder to merge itinto that CRL."/>
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23 <param name="min_locus_size" type="integer" value="5" label="Minimum locus size" min="1"
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24 help="Minimum number of reads a locus should have in order to participate in CRL creation.
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25 Always set this value relative to your sequencing depth. Setting this to lower leads
f7cce908ef9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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26 CRLs of random multimappings Also consider setting the --crl_share option
f7cce908ef9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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27 along with this"/>
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28 <param name="em_threshold" type="float" value="1" label="EM threshold"
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29 help="The maximum difference of transcripts expression between two consecutive iterations of EM algorithm to converge."/>
f7cce908ef9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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30 <param name="crl" type="boolean" truevalue="-crl" falsevalue="" checked="true"
f7cce908ef9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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31 label="Create CRLs" help="Create CRLs and qunatify them or use the loci further without creating the CRLs" />
f7cce908ef9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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32 </inputs>
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33 <outputs>
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34 <data format="tabular" name="loci" from_work_dir="loci.counts" label="ChiRA quantified loci on ${on_string}"/>
f7cce908ef9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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35 </outputs>
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36
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37 <tests>
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38 <test expect_num_outputs="1">
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39 <param name="segments" value="segments.bed"/>
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40 <param name="merged" value="merged.bed"/>
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41 <output name="loci" file="loci.counts"/>
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42 </test>
f7cce908ef9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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43 </tests>
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44
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45 <help>
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46
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47 .. class:: infomark
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48
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49 **What it does**
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50
f7cce908ef9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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51 This tool first creates CRLS from merged BED file and quantifies them based on the mapped reads.
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52
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53 **Inputs**
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54
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55 * A BED file containing alignment segments
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56 * A BED file containing merged alignments
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57
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58 **Output**
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59
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60 * Tabular file containing the reads and their CRLs with TPM values.
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61
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62 </help>
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63 <expand macro="citations" />
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64 </tool>