Mercurial > repos > iuc > tximport
annotate tximport.xml @ 2:1906cb429215 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b443b4cc23849e6d37ae82b0b86d60687d3f961f"
author | iuc |
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date | Tue, 09 Nov 2021 22:44:59 +0000 |
parents | 2c338211927c |
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rev | line source |
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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"
iuc
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2 <macros> |
2
1906cb429215
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b443b4cc23849e6d37ae82b0b86d60687d3f961f"
iuc
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3 <token name="@TOOL_VERSION@">1.22.0</token> |
1
2c338211927c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
iuc
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4 </macros> |
0
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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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"
iuc
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6 <xrefs> |
2c338211927c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
iuc
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7 <xref type="bio.tools">tximport</xref> |
2c338211927c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
iuc
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8 </xrefs> |
0
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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9 <requirements> |
1
2c338211927c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
iuc
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10 <requirement type="package" version="@TOOL_VERSION@">bioconductor-tximport</requirement> |
2
1906cb429215
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b443b4cc23849e6d37ae82b0b86d60687d3f961f"
iuc
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11 <requirement type="package" version="1.46.1">bioconductor-genomicfeatures</requirement> |
1
2c338211927c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
iuc
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12 <requirement type="package" version="1.20.3">r-getopt</requirement> |
0
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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13 </requirements> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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14 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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15 <stdio> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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16 <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
parents:
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17 <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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18 source="both" |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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19 level="fatal" |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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20 description="Execution halted." /> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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21 </stdio> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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22 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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23 <command><![CDATA[ |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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24 #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
parents:
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25 #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
parents:
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26 #if $gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.mapping_file_option == 'gff_gtf': |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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27 ln -s '$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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28 #else: |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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29 ln -s '$gene_id_source_selector.gff_source_selector.gff_tx2gene_selector.own_tx2gene' mapping.tab && |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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30 #end if |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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31 #end if |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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32 #end if |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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33 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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34 Rscript '${__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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35 --format $input_source_selector.input_source |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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36 #if $input_source_selector.input_source == 'none': |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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37 --txIdCol '$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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38 --abundanceCol '$input_source_selector.abundance_col' |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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39 --countsCol '$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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40 --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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41 #end if |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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42 #if $gene_id_source_selector.gene_id_source == 'gene_id_column_option': |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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43 --geneIdCol '$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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44 #else |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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45 #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
parents:
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46 #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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47 --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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48 #else |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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49 --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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50 #end if |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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51 #else: |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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52 --tx2gene $gene_id_source_selector.gff_source_selector.tx2gene.fields.path |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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53 #end if |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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54 #end if |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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55 --countsFiles '$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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56 --countsFromAbundance $counts_from_abundance |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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57 --out_file '${gene_level_values}' |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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58 ]]></command> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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59 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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60 <configfiles> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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61 <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"
iuc
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62 #for $file in $counts_file: |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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63 #echo str($file.element_identifier) + "\t" + str($file) + "\n" |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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64 #end for]]></configfile> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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65 </configfiles> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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66 <inputs> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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67 <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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68 <conditional name="input_source_selector"> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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69 <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"
iuc
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70 <option value="salmon" selected="True">Salmon</option> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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71 <option value="sailfish">Sailfish</option> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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72 <option value="alevin">Alevin</option> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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73 <option value="kallisto">Kallisto</option> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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74 <option value="rsem">RSEM</option> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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75 <option value="stringtie">Stringtie</option> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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76 <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"
iuc
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77 </param> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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78 <when value="none"> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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79 <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"
iuc
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80 <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"
iuc
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81 <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"
iuc
parents:
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82 <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"
iuc
parents:
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83 </when> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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84 <when value="salmon"/> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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85 <when value="sailfish"/> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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86 <when value="alevin"/> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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87 <when value="kallisto"/> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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88 <when value="rsem"/> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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89 <when value="stringtie"/> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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90 </conditional> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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91 <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:
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92 <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:
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93 <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:
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94 <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:
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95 </param> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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96 <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:
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97 <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:
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98 </when> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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99 <when 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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100 <conditional name="gff_source_selector"> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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101 <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
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102 <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
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103 <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:
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104 </param> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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105 <when value="built-in"> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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106 <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
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107 <options from_data_table="tx2gene_table"> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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108 <filter type="sort_by" column="1"/> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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109 <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"
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110 </options> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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111 </param> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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112 </when> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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113 <when value="history"> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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114 <conditional name="gff_tx2gene_selector"> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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115 <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
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116 <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
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117 <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
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118 </param> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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119 <when value="gff_gtf"> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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120 <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
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121 </when> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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122 <when value="tx2gene"> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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123 <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:
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124 </when> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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125 </conditional> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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126 </when> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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127 </conditional> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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128 </when> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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129 </conditional> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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130 <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
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131 <option value="no">No</option> |
1
2c338211927c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
iuc
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0
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132 <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
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0
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133 <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
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0
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134 <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
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135 </param> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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136 </inputs> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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137 <outputs> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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138 <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
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139 </outputs> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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140 |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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141 <tests> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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142 <test> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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143 <param name="input_source" value="salmon"/> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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144 <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
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145 <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:
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146 <param name="gff_source" value="history"/> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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147 <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
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148 <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
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149 <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
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150 <output name="gene_level_values"> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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151 <assert_contents> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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152 <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
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153 <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
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154 </assert_contents> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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155 </output> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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156 </test> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
parents:
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157 <test> |
206a71a69161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
iuc
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158 <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:
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159 <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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160 <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:
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161 <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:
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|
162 <param name="mapping_file_option" value="gff_gtf"/> |
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163 <param name="own_gff" value="Araport11_subset.gff3"/> |
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164 <param name="counts_file" value="salmon_sample2.tab,salmon_sample1.tab" /> |
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165 <output name="gene_level_values"> |
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166 <assert_contents> |
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167 <has_text_matching expression="salmon_sample2.tab\tsalmon_sample1.tab" /> |
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168 <has_text_matching expression="AT1G01010\t156\t156" /> |
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169 </assert_contents> |
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170 </output> |
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171 </test> |
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172 <test> |
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173 <param name="input_source" value="salmon"/> |
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174 <param name="gene_id_source" value="external_file"/> |
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175 <param name="counts_from_abundance" value="no"/> |
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176 <param name="gff_source" value="built-in"/> |
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177 <param name="tx2gene" value="Ath_Araport11_subset"/> |
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178 <param name="counts_file" value="salmon_sample2.tab,salmon_sample1.tab" /> |
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179 <output name="gene_level_values"> |
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180 <assert_contents> |
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181 <has_text_matching expression="salmon_sample2.tab\tsalmon_sample1.tab" /> |
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182 <has_text_matching expression="AT1G01010\t156\t156" /> |
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183 </assert_contents> |
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184 </output> |
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185 </test> |
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186 <!-- Test input with custom format --> |
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187 <test> |
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188 <param name="input_source" value="none"/> |
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189 <param name="tx_id_col" value="Transcript_id_here"/> |
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190 <param name="abundance_col" value="Abundance_goes_here"/> |
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191 <param name="counts_col" value="Here_goes_the_counts"/> |
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192 <param name="length_col" value="Here_goes_the_length"/> |
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193 <param name="counts_from_abundance" value="no"/> |
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194 <param name="gff_source" value="built-in"/> |
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195 <param name="tx2gene" value="Ath_Araport11_subset"/> |
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196 <param name="counts_file" value="custom_sample.tab" /> |
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197 <output name="gene_level_values"> |
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198 <assert_contents> |
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199 <has_text_matching expression="custom_sample.tab" /> |
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200 <has_text_matching expression="AT1G01010\t156" /> |
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201 </assert_contents> |
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202 </output> |
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203 </test> |
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204 </tests> |
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205 <help><![CDATA[ |
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206 .. class:: infomark |
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207 |
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208 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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209 Take into account that DEseq2 package in Galaxy requires one table per sample. |
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210 ]]></help> |
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211 <citations> |
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212 <citation type="doi">doi:10.18129/B9.bioc.tximport</citation> |
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213 </citations> |
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214 </tool> |