Mercurial > repos > iuc > kallisto_pseudo

annotate kallisto_pseudo.xml @ 0:2953303df011 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
author iuc
date Tue, 22 Aug 2017 04:16:08 -0400
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children 1c75aa5de15e
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2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
1 <?xml version="1.0"?>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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2 <tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.0">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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3 <description>- run pseudoalignment on RNA-Seq transcripts</description>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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4 <macros>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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5 <import>macros.xml</import>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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6 </macros>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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7 <expand macro="requirements" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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8 <command detect_errors="exit_code">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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9 <![CDATA[
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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10 #if $reference_genome.reference_genome_source == "history":
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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11 ln -s '$reference_genome.reference' reference.fa &&
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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12 kallisto index reference.fa -i reference.kallisto &&
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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13 #set index_path = 'reference.kallisto'
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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14 #else:
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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15 #set index_path = $reference_genome.index.fields.path
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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16 #end if
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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17 kallisto pseudo -i '$index_path'
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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18 #if $pseudobam:
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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19 $pseudobam -o .
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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20 #else:
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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21 --threads \${GALAXY_SLOTS:-1}
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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22 -o .
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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23 #end if
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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24
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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25
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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26 #if str($single_paired.single_paired_selector) == 'single':
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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27 --single --fragment-length $single_paired.fragment_length
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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28 --sd $single_paired.sd '$single_paired.reads'
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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29 #else:
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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30 #if str($single_paired.collection.collection_selector) == 'collection':
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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31 '$single_paired.collection.reads.forward'
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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32 '$single_paired.collection.reads.reverse'
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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33 #else:
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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34 #if str($single_paired.collection.fastq_umi.umi) == 'yes':
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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35 --batch '$batch' --umi
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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36 #else:
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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37 '$single_paired.collection.fastq_umi.forward'
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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38 '$single_paired.collection.fastq_umi.reverse'
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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39 #end if
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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40 #end if
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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41 #end if
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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42 #if $pseudobam:
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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43 | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o '$pseudobam_output' -
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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44 #end if
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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45 && if [ -f run_info.json ] ; then cat run_info.json ; fi &&
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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46 mkdir outputs &&
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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47 if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi &&
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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48 if [ -f matrix.tsv ] ; then mv matrix.tsv outputs/Matrix.tabular ; fi &&
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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49 if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi &&
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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50 if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi &&
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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51 if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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52 ]]>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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53 </command>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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54 <configfiles>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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55 <configfile name="batch">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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56 <![CDATA[
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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57 #if str($single_paired.single_paired_selector) == 'single':
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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58 cell1 $single_paired.reads
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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59 #else:
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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60 #if str($single_paired.collection.collection_selector) == 'collection':
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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61 cell1 $single_paired.collection.reads.forward $single_paired.collection.reads.reverse
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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62 #else:
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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63 cell1 $single_paired.collection.fastq_umi.forward $single_paired.collection.fastq_umi.reverse
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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64 #end if
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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65 #end if
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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66 ]]>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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67 </configfile>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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68 </configfiles>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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69 <inputs>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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70 <conditional name="reference_genome">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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71 <param name="reference_genome_source" type="select" label="Reference genome for pseudoalignment">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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72 <option value="indexed" selected="true">Use a built-in genome</option>
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73 <option value="history">Use a genome from history</option>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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74 </param>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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75 <when value="indexed">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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76 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy administrator">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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77 <options from_data_table="kallisto_indexes">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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78 <filter type="sort_by" column="2" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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79 <validator type="no_options" message="No genomes are available for the selected input dataset" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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80 </options>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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81 </param>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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82 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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83 <when value="history">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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84 <param name="reference" type="data" format="fasta" label="FASTA reference genome" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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85 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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86 </conditional>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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87 <conditional name="single_paired">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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88 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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89 <option value="single" selected="true">Single-end</option>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
90 <option value="paired">Paired</option>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
91 </param>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
92 <when value="single">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
93 <param name="reads" type="data" format="fastq" multiple="True" label="Reads in FASTQ format" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
94 <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
95 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
96 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
97 <when value="paired">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
98 <conditional name="collection">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
99 <param name="collection_selector" type="select" label="Collection or individual datasets">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
100 <option value="datasets" selected="true">Individual files</option>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
101 <option value="collection">Pair or list of pairs</option>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
102 </param>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
103 <when value="datasets">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
104 <conditional name="fastq_umi">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
105 <param name="umi" type="select" label="Pseudoalignment uses UMIs">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
106 <option value="no" selected="true">Paired FASTQ</option>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
107 <option value="yes">UMI</option>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
108 </param>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
109 <when value="yes">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
110 <param name="forward" type="data" format="tabular" multiple="True" label="UMI file" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
111 <param name="reverse" type="data" format="fastq" multiple="True" label="FASTQ reads" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
112 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
113 <when value="no">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
114 <param name="forward" type="data" format="fastq" multiple="True" label="Forward reads" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
115 <param name="reverse" type="data" format="fastq" multiple="True" label="Reverse reads" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
116 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
117 </conditional>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
118 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
119 <when value="collection">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
120 <param name="reads" type="data_collection" format="fastq" collection_type="paired" label="Collection of reads" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
121 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
122 </conditional>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
123 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
124 </conditional>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
125 <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
126 </inputs>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
127 <outputs>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
128 <data format="tabular" name="sample">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
129 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="outputs" ext="tabular" visible="true" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
130 </data>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
131 <data format="bam" name="pseudobam_output" label="${tool.name} on ${on_string}: Pseudoalignments (BAM)">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
132 <filter>pseudobam</filter>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
133 </data>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
134 </outputs>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
135 <tests>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
136 <test>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
137 <param name="reference_genome_source" value="history" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
138 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
139 <param name="single_paired_selector" value="paired" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
140 <param name="collection_selector" value="datasets" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
141 <param name="umi" value="yes" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
142 <param name="forward" ftype="tabular" value="mm10_chrM.umi" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
143 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
144 <output name="sample">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
145 <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out1.tab" ftype="tabular" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
146 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out1.ec" ftype="tabular" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
147 <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out1.cells" ftype="tabular" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
148 </output>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
149 </test>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
150 <test>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
151 <param name="reference_genome_source" value="history" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
152 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
153 <param name="single_paired_selector" value="paired" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
154 <param name="collection_selector" value="collection" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
155 <param name="umi" value="no" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
156 <param name="reads">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
157 <collection type="paired">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
158 <element name="forward" value="mm10_chrM-1.f.fq" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
159 <element name="reverse" value="mm10_chrM-1.r.fq" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
160 </collection>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
161 </param>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
162 <output name="sample">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
163 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out2.tab" ftype="tabular" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
164 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out2.ec" ftype="tabular" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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165 </output>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
166 </test>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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167 <test>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
168 <param name="reference_genome_source" value="history" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
169 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
170 <param name="single_paired_selector" value="single" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
171 <param name="collection_selector" value="collection" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
172 <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff changeset
173 <output name="sample">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
174 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out3.tab" ftype="tabular" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
175 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out3.ec" ftype="tabular" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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176 </output>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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177 </test>
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178 <test>
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179 <param name="reference_genome_source" value="history" />
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180 <param name="reference" ftype="fasta" value="felCat8_chrM.fa" />
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181 <param name="single_paired_selector" value="paired" />
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182 <param name="collection_selector" value="datasets" />
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183 <param name="umi" value="no" />
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184 <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />
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185 <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />
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186 <output name="sample">
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187 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out4.tab" ftype="tabular" />
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188 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out4.ec" ftype="tabular" />
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189 </output>
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190 </test>
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191 <test>
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192 <param name="reference_genome_source" value="cached" />
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193 <param name="single_paired_selector" value="paired" />
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194 <param name="collection_selector" value="datasets" />
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195 <param name="pseudobam" value="true" />
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196 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
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197 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />
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198 <output name="sample">
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199 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out5.tab" ftype="tabular" />
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200 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out5.ec" ftype="tabular" />
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201 </output>
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202 <output name="pseudobam_output" file="kallisto_pseudo_out5.bam" ftype="bam" />
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203 </test>
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204 <test>
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205 <param name="reference_genome_source" value="cached" />
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206 <param name="single_paired_selector" value="paired" />
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207 <param name="collection_selector" value="datasets" />
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208 <param name="umi" value="yes" />
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209 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" />
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210 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />
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211 <output name="sample">
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212 <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" />
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213 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out6.ec" ftype="tabular" />
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214 <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out6.cells" ftype="tabular" />
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215 </output>
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216 </test>
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217 </tests>
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218 <help>
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219 <![CDATA[
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220 `kallisto <https://pachterlab.github.io/kallisto/manual>`__ is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
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221 ]]>
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222 </help>
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223 <expand macro="citations" />
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224 </tool>