Mercurial > repos > iuc > tximport

annotate tximport.xml @ 0:206a71a69161 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
author iuc
date Wed, 04 Dec 2019 05:57:26 -0500
parents
children 2c338211927c
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0
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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1 <tool id="tximport" name="tximport" version="0.1">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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2 <description>Summarize transcript-level estimates for gene-level analysis</description>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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3 <requirements>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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4 <requirement type="package">bioconductor-tximport</requirement>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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5 <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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6 <requirement type="package" version="1.20.2">r-getopt</requirement>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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7 </requirements>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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8
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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9 <stdio>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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10 <exit_code range="1:" level="fatal" description="Error code returned" />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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11 <regex match="is not TRUE"
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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12 source="both"
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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13 level="fatal"
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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14 description="Execution halted." />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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15 </stdio>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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16
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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17 <command><![CDATA[
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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18 #if $gene_id_source_selector.gene_id_source == 'external_file':
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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19 #if $gene_id_source_selector.gff_source_selector.gff_source == 'history':
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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20 #if $gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.mapping_file_option == 'gff_gtf':
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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21 ln -s '$gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.own_gff' mapping.gff &&
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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22 #else:
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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23 ln -s '$gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.own_tx2gene' mapping.tab &&
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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24 #end if
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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25 #end if
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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26 #end if
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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27
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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28 Rscript '${__tool_directory__}/tximport.R'
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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29 --format $input_source_selector.input_source
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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30 #if $input_source_selector.input_source == 'none':
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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31 --txIdCol '$input_source_selector.tx_id_col'
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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32 --abundanceCol '$input_source_selector.abundance_col'
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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33 --countsCol '$input_source_selector.counts_col'
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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34 --lengthCol '$input_source_selector.length_col'
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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35 #end if
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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36 #if $gene_id_source_selector.gene_id_source == 'gene_id_column_option':
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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37 --geneIdCol '$gene_id_source_selector.gene_id_column'
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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38 #else
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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39 #if $gene_id_source_selector.gff_source_selector.gff_source == "history":
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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40 #if $gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.mapping_file_option == 'tx2gene':
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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41 --tx2gene mapping.tab
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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42 #else
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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43 --gff_file mapping.gff
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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44 #end if
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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45 #else:
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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46 --tx2gene $gene_id_source_selector.gff_source_selector.tx2gene.fields.path
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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47 #end if
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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48 #end if
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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49 --countsFiles '$counts_files_table'
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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50 --countsFromAbundance $counts_from_abundance
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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51 --out_file '${gene_level_values}'
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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52 ]]></command>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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53
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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54 <configfiles>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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55 <configfile name="counts_files_table"><![CDATA[#echo "sample_id\tpath\n"
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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56 #for $file in $counts_file:
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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57 #echo str($file.element_identifier) + "\t" + str($file) + "\n"
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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58 #end for]]></configfile>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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59 </configfiles>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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60 <inputs>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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61 <param name="counts_file" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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62 <conditional name="input_source_selector">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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63 <param name="input_source" type ="select" label="Select the source of the quantification file">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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64 <option value="salmon" selected="True">Salmon</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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65 <option value="sailfish">Sailfish</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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66 <option value="alevin">Alevin</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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67 <option value="kallisto">Kallisto</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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68 <option value="rsem">RSEM</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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69 <option value="stringtie">Stringtie</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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70 <option value="none">Custom format (specify the columns)</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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71 </param>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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72 <when value="none">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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73 <param name="tx_id_col" type="text" label="Name of the txID columns"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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74 <param name="abundance_col" type="text" label="Name of the abundance column"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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75 <param name="counts_col" type="text" label="Name of the counts column"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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76 <param name="length_col" type="text" label="Name of the length column"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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77 </when>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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78 <when value="salmon"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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79 <when value="sailfish"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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80 <when value="alevin"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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81 <when value="kallisto"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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82 <when value="rsem"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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83 <when value="stringtie"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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84 </conditional>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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85 <conditional name="gene_id_source_selector" >
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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86 <param name="gene_id_source" type="select" label="Is the gene id part of the counts file or will be obtained from an external file?">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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87 <option value="external_file" selected="True">Use an external file to map transcript to gene ids</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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diff changeset
88 <option value="gene_id_column_option">Gene id is a column of the input file</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
89 </param>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
90 <when value="gene_id_column_option">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
91 <param name="gene_id_column" type="text" label="Name of the column containing the geneID"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
92 </when>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
93 <when value="external_file">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
94 <conditional name="gff_source_selector">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
95 <param name="gff_source" type="select" label="Select a tx-to-gene table/GFF from your history or use a built-in file?">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
96 <option value="built-in" selected="True">Use a built-in file</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
97 <option value="history" >Use one from the history</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
98 </param>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
99 <when value="built-in">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
100 <param name="tx2gene" type="select" label="Select an annotation version" help="If the build of your interest is not listed contact your Galaxy admin">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
101 <options from_data_table="tx2gene_table">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
102 <filter type="sort_by" column="1"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
103 <validator type="no_options" message="No files are available for the selected input dataset"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
104 </options>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
105 </param>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
106 </when>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
107 <when value="history">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
108 <conditional name="gff_tx2gene_selector">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
109 <param name="mapping_file_option" type="select" label="Will you provide a tx2gene or a GFF/GTF file?">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
110 <option value="tx2gene" selected="True">TranscriptID to GeneID table</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
111 <option value="gff_gtf">GTF/GFF file</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
112 </param>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
113 <when value="gff_gtf">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
114 <param name="own_gff" type="data" format="gff" label="Select your GFF file"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
115 </when>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
116 <when value="tx2gene">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
117 <param name="own_tx2gene" type="data" format="tabular" label="Select your TranscriptID to GeneID table file"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
118 </when>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
119 </conditional>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
120 </when>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
121 </conditional>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
122 </when>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
123 </conditional>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
124 <param name="counts_from_abundance" type="select" label="Summarization using the abundance (TPM) values?">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
125 <option value="no">No</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
126 <option value="scaled_TPM">Scaled up to library size</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
127 <option value="length_scaled_TPM">Scaled using the avg. transcript legth over samples and then the library size</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
128 <option value="dtu_scaled_TPM">Scaled using the median transcript length among isoforms of a gene, and then the library size</option>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
129 </param>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
130 </inputs>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
131 <outputs>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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diff changeset
132 <data name="gene_level_values" format="tabular" label="Gene level summarization on ${on_string}"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
133 </outputs>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
134
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
135 <tests>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
136 <test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
137 <param name="input_source" value="salmon"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
138 <param name="gene_id_source" value="external_file"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
139 <param name="counts_from_abundance" value="no"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
140 <param name="gff_source" value="history"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
141 <param name="mapping_file_option" value="tx2gene"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
142 <param name="own_tx2gene" value="tx2gene.tab"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
143 <param name="counts_file" value="salmon_sample2.tab,salmon_sample1.tab" />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
144 <output name="gene_level_values">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
145 <assert_contents>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
146 <has_text_matching expression="salmon_sample2.tab\tsalmon_sample1.tab" />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
147 <has_text_matching expression="AT1G01010\t156\t156" />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
148 </assert_contents>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
149 </output>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
150 </test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
151 <test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
152 <param name="input_source" value="salmon"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
153 <param name="gene_id_source" value="external_file"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
154 <param name="counts_from_abundance" value="no"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
155 <param name="gff_source" value="history"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
156 <param name="mapping_file_option" value="gff_gtf"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
157 <param name="own_gff" value="Araport11_subset.gff3"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
158 <param name="counts_file" value="salmon_sample2.tab,salmon_sample1.tab" />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
159 <output name="gene_level_values">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
160 <assert_contents>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
161 <has_text_matching expression="salmon_sample2.tab\tsalmon_sample1.tab" />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
162 <has_text_matching expression="AT1G01010\t156\t156" />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
163 </assert_contents>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
164 </output>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
165 </test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
166 <test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
167 <param name="input_source" value="salmon"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
168 <param name="gene_id_source" value="external_file"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
169 <param name="counts_from_abundance" value="no"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
170 <param name="gff_source" value="built-in"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
171 <param name="tx2gene" value="Ath_Araport11_subset"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
172 <param name="counts_file" value="salmon_sample2.tab,salmon_sample1.tab" />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
173 <output name="gene_level_values">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
174 <assert_contents>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
175 <has_text_matching expression="salmon_sample2.tab\tsalmon_sample1.tab" />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
176 <has_text_matching expression="AT1G01010\t156\t156" />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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177 </assert_contents>
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178 </output>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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179 </test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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180 <!-- Test input with custom format -->
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181 <test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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182 <param name="input_source" value="none"/>
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183 <param name="tx_id_col" value="Transcript_id_here"/>
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184 <param name="abundance_col" value="Abundance_goes_here"/>
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185 <param name="counts_col" value="Here_goes_the_counts"/>
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186 <param name="length_col" value="Here_goes_the_length"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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187 <param name="counts_from_abundance" value="no"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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188 <param name="gff_source" value="built-in"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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189 <param name="tx2gene" value="Ath_Araport11_subset"/>
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190 <param name="counts_file" value="custom_sample.tab" />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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191 <output name="gene_level_values">
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192 <assert_contents>
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193 <has_text_matching expression="custom_sample.tab" />
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194 <has_text_matching expression="AT1G01010\t156" />
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195 </assert_contents>
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196 </output>
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197 </test>
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198 </tests>
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199 <help><![CDATA[
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200 .. class:: infomark
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201
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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202 Current version only works in 'merge' mode: A single table of gene summarizations is generated with one column for each sample file.
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203 Take into account that DEseq2 package in Galaxy requires one table per sample.
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204 ]]></help>
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205 <citations>
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206 <citation type="doi">doi:10.18129/B9.bioc.tximport</citation>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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207 </citations>
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208 </tool>