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annotate salmonquantmerge.xml @ 10:42628a3010d4 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1
author bgruening
date Fri, 31 Oct 2025 19:16:59 +0000
parents 58b9ef13fcca
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664
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1 <tool id="salmonquantmerge" name="Salmon quantmerge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">
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2 <description>Merge multiple quantification results into a single file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements"/>
9
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"><![CDATA[
9
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10 #import re
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11
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12 #for $counter, $input_data in enumerate($quantfiles):
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13 rank_of_series=$counter
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14 mkdir ${counter}.quantmerge &&
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15 ln -s '$input_data.quants' ${counter}.quantmerge/quant.sf &&
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16 #end for
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17 salmon --no-version-check quantmerge
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18 --quants *.quantmerge
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19 --names
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20 #for $counter, $input_data in enumerate($quantfiles):
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21 #if $input_data.names and re.sub(' ', '', '$input_data.names') != '':
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22 '${input_data.names}'
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23 #else:
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24 #set $identifier=re.sub('[^\w\-\s]', '_', str($input_data.quants.element_identifier))
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25 "$identifier"
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26 #end if
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27 #end for
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28 --column '${column}'
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29 ${genes}
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30 #if $missing:
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31 --missing '${missing}'
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32 #end if
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33 -o qmergeout.tab
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34 ]]></command>
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35 <inputs>
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36 <repeat name="quantfiles" title="Quant file and names">
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37 <param argument="--quants" type="data" format="tsv,tabular" label="Salmon quant tabular output files"/>
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38 <param argument="--names" type="text" label="One-word sample names" optional="True"/>
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39 </repeat>
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40 <param argument="--column" type="select" label="Columns" help="Name of columns that will be merged in the output file">
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41 <option value="len" selected="True">Length</option>
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42 <option value="elen">Effective Length</option>
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43 <option value="tpm">Transcripts per Million</option>
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44 <option value="numreads">NumReads</option>
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45 </param>
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46 <param argument="--genes" type="boolean" truevalue="--genes" falsevalue="" checked="False" label="Genes" help="Use gene quantifications instead of transcript"/>
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47 <param argument="--missing" type="integer" label="Missing" optional="True" help="The value of missing values"/>
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48 </inputs>
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49 <outputs>
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50 <data name="mergedfile" format="tabular" label="${tool.name} on ${on_string}" from_work_dir="qmergeout.tab"/>
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51 </outputs>
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52 <tests>
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53 <test expect_num_outputs="1">
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54 <repeat name="quantfiles">
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55 <param name="quants" value="quant2.sf"/>
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56 <param name="names" value="asdf"/>
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57 </repeat>
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58 <repeat name="quantfiles">
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59 <param name="quants" value="quant1.sf"/>
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60 <param name="names" value="qwerty"/>
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61 </repeat>
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62 <output name="mergedfile" ftype="tabular">
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63 <assert_contents>
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64 <has_text text="qwerty"/>
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65 <has_text text="NM_014621"/>
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66 <has_n_columns n="3"/>
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67 </assert_contents>
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68 </output>
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69 </test>
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70 </tests>
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71 <help><![CDATA[
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72 @salmonhelp@
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73 ]]></help>
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74 <expand macro="citations"/>
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75 </tool>