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annotate tximport.xml @ 3:0bcc35b10569 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 5f8e6e70a9d82331367f7a052a76a04c47c5144e
author iuc
date Sat, 28 Sep 2024 16:33:19 +0000
parents 1906cb429215
children
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2c338211927c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
iuc
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1 <tool id="tximport" name="tximport" version="@TOOL_VERSION@" profile="20.09">
2c338211927c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
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2 <macros>
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0bcc35b10569 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 5f8e6e70a9d82331367f7a052a76a04c47c5144e
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3 <token name="@TOOL_VERSION@">1.30.0</token>
1
2c338211927c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
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4 </macros>
0
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5 <description>Summarize transcript-level estimates for gene-level analysis</description>
1
2c338211927c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
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6 <xrefs>
2c338211927c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
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7 <xref type="bio.tools">tximport</xref>
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0bcc35b10569 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 5f8e6e70a9d82331367f7a052a76a04c47c5144e
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8 <xref type="bioconductor">tximport</xref>
1
2c338211927c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
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9 </xrefs>
0
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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10 <requirements>
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2c338211927c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
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11 <requirement type="package" version="@TOOL_VERSION@">bioconductor-tximport</requirement>
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0bcc35b10569 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 5f8e6e70a9d82331367f7a052a76a04c47c5144e
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12 <requirement type="package" version="1.54.1">bioconductor-genomicfeatures</requirement>
0bcc35b10569 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 5f8e6e70a9d82331367f7a052a76a04c47c5144e
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13 <requirement type="package" version="1.20.4">r-getopt</requirement>
0
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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14 </requirements>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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16 <stdio>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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17 <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"
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18 <regex match="is not TRUE"
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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19 source="both"
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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20 level="fatal"
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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21 description="Execution halted." />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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22 </stdio>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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24 <command><![CDATA[
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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25 #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"
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26 #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"
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27 #if $gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.mapping_file_option == 'gff_gtf':
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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28 ln -s '$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"
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29 #else:
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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30 ln -s '$gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.own_tx2gene' mapping.tab &&
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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31 #end if
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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32 #end if
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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33 #end if
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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34
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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35 Rscript '${__tool_directory__}/tximport.R'
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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36 --format $input_source_selector.input_source
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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37 #if $input_source_selector.input_source == 'none':
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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38 --txIdCol '$input_source_selector.tx_id_col'
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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39 --abundanceCol '$input_source_selector.abundance_col'
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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40 --countsCol '$input_source_selector.counts_col'
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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41 --lengthCol '$input_source_selector.length_col'
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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42 #end if
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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43 #if $gene_id_source_selector.gene_id_source == 'gene_id_column_option':
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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44 --geneIdCol '$gene_id_source_selector.gene_id_column'
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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45 #else
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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46 #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"
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47 #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"
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48 --tx2gene mapping.tab
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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49 #else
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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50 --gff_file mapping.gff
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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51 #end if
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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52 #else:
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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53 --tx2gene $gene_id_source_selector.gff_source_selector.tx2gene.fields.path
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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54 #end if
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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55 #end if
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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56 --countsFiles '$counts_files_table'
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57 --countsFromAbundance $counts_from_abundance
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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58 --out_file '${gene_level_values}'
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59 ]]></command>
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60
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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61 <configfiles>
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62 <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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63 #for $file in $counts_file:
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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64 #echo str($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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65 #end for]]></configfile>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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66 </configfiles>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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67 <inputs>
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68 <param name="counts_file" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
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69 <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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70 <param name="input_source" type ="select" label="Select the source of the quantification file">
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71 <option value="salmon" selected="True">Salmon</option>
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72 <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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73 <option value="alevin">Alevin</option>
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74 <option value="kallisto">Kallisto</option>
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75 <option value="rsem">RSEM</option>
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76 <option value="stringtie">Stringtie</option>
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77 <option value="none">Custom format (specify the columns)</option>
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78 </param>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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79 <when value="none">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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80 <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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81 <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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82 <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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83 <param name="length_col" type="text" label="Name of the length column"/>
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84 </when>
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85 <when value="salmon"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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86 <when value="sailfish"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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87 <when value="alevin"/>
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iuc
parents:
diff changeset
88 <when value="kallisto"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
89 <when value="rsem"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
90 <when value="stringtie"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
91 </conditional>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
92 <conditional name="gene_id_source_selector" >
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
93 <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"
iuc
parents:
diff changeset
94 <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"
iuc
parents:
diff changeset
95 <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
96 </param>
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iuc
parents:
diff changeset
97 <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
98 <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
99 </when>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
100 <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
101 <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
102 <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
103 <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
104 <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
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 value="built-in">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
107 <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
108 <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
109 <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
110 <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
111 </options>
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>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
114 <when value="history">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
115 <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
116 <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
117 <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
118 <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
119 </param>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
120 <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
121 <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
122 </when>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
123 <when value="tx2gene">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
124 <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
125 </when>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
126 </conditional>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
127 </when>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
128 </conditional>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
129 </when>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
130 </conditional>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
131 <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
132 <option value="no">No</option>
1
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iuc
parents: 0
diff changeset
133 <option value="scaledTPM">Scaled up to library size</option>
2c338211927c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
iuc
parents: 0
diff changeset
134 <option value="lengthScaledTPM">Scaled using the avg. transcript legth over samples and then the library size</option>
2c338211927c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
iuc
parents: 0
diff changeset
135 <option value="dtuScaledTPM">Scaled using the median transcript length among isoforms of a gene, and then the library size</option>
0
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
136 </param>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
137 </inputs>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
138 <outputs>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
139 <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
140 </outputs>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
141
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
142 <tests>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
143 <test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
144 <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
145 <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
146 <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
147 <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
148 <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
149 <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
150 <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
151 <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
152 <assert_contents>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
153 <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
154 <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
155 </assert_contents>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
156 </output>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
157 </test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
158 <test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
159 <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
160 <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
161 <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
162 <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
163 <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
164 <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
165 <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
166 <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
167 <assert_contents>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
168 <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
169 <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
170 </assert_contents>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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parents:
diff changeset
171 </output>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
172 </test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
173 <test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
diff changeset
174 <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
175 <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:
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176 <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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177 <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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178 <param name="tx2gene" value="Ath_Araport11_subset"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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179 <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"
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180 <output name="gene_level_values">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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181 <assert_contents>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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182 <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"
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183 <has_text_matching expression="AT1G01010\t156\t156" />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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184 </assert_contents>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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185 </output>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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186 </test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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187 <!-- Test input with custom format -->
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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188 <test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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189 <param name="input_source" value="none"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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190 <param name="tx_id_col" value="Transcript_id_here"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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191 <param name="abundance_col" value="Abundance_goes_here"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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192 <param name="counts_col" value="Here_goes_the_counts"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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193 <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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194 <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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195 <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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196 <param name="tx2gene" value="Ath_Araport11_subset"/>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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197 <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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198 <output name="gene_level_values">
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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199 <assert_contents>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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200 <has_text_matching expression="custom_sample.tab" />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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201 <has_text_matching expression="AT1G01010\t156" />
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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202 </assert_contents>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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203 </output>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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204 </test>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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205 </tests>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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206 <help><![CDATA[
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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207 .. class:: infomark
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208
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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209 Current version only works in 'merge' mode: A single table of gene summarizations is generated with one column for each sample file.
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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210 Take into account that DEseq2 package in Galaxy requires one table per sample.
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211 ]]></help>
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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212 <citations>
3
0bcc35b10569 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 5f8e6e70a9d82331367f7a052a76a04c47c5144e
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213 <citation type="doi">10.18129/B9.bioc.tximport</citation>
0
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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214 </citations>
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215 </tool>