Mercurial > repos > iuc > kallisto_pseudo

annotate kallisto_pseudo.xml @ 4:01247aaf0a10 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 94e4019f3e5e81d3a09cd92ce1e93587600847d8"
author iuc
date Tue, 06 Apr 2021 21:08:39 +0000
parents 5ae5c312d718
children 87c11c05d238
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2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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1 <?xml version="1.0"?>
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01247aaf0a10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 94e4019f3e5e81d3a09cd92ce1e93587600847d8"
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2 <tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.2">
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2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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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
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4 <macros>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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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
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6 </macros>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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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
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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
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9 <![CDATA[
2
1c75aa5de15e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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10 #if $reference_transcriptome.reference_transcriptome_source == "history":
1c75aa5de15e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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11 ln -s '$reference_transcriptome.reference' reference.fa &&
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2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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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
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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
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14 #else:
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1c75aa5de15e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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15 #set index_path = $reference_transcriptome.index.fields.path
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16 #end if
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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17 kallisto pseudo -i '$index_path'
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18 --threads \${GALAXY_SLOTS:-1}
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19 -o .
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2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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21 #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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22 --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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23 --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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24 #else:
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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25 #if str($single_paired.collection.collection_selector) == 'collection':
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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26 '$single_paired.collection.reads.forward'
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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27 '$single_paired.collection.reads.reverse'
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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28 #else:
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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29 #if str($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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30 --batch '$batch' --umi
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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31 #else:
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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32 '$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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33 '$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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34 #end if
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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35 #end if
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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36 #end if
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37 && 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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38 mkdir outputs &&
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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39 if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi &&
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40 if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi &&
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2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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41 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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42 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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43 if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi
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44 ]]>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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45 </command>
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46 <configfiles>
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47 <configfile name="batch">
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48 <![CDATA[
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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49 #if str($single_paired.single_paired_selector) == 'single':
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50 cell1 $single_paired.reads
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51 #else:
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52 #if str($single_paired.collection.collection_selector) == 'collection':
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53 cell1 $single_paired.collection.reads.forward $single_paired.collection.reads.reverse
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54 #else:
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55 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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56 #end if
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57 #end if
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58 ]]>
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59 </configfile>
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60 </configfiles>
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61 <inputs>
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62 <expand macro="reference_input" />
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63 <conditional name="single_paired">
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64 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
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65 <option value="single" selected="true">Single-end</option>
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66 <option value="paired">Paired</option>
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67 </param>
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68 <when value="single">
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69 <param name="reads" type="data" format="fastq,fastq.gz" multiple="True" label="Reads in FASTQ format" />
0
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70 <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" />
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71 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
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72 </when>
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73 <when value="paired">
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74 <conditional name="collection">
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75 <param name="collection_selector" type="select" label="Collection or individual datasets">
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76 <option value="datasets" selected="true">Individual files</option>
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77 <option value="collection">Pair or list of pairs</option>
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78 </param>
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79 <when value="datasets">
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80 <conditional name="fastq_umi">
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81 <param name="umi" type="select" label="Pseudoalignment uses UMIs">
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82 <option value="no" selected="true">Paired FASTQ</option>
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83 <option value="yes">UMI</option>
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84 </param>
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85 <when value="yes">
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86 <param name="forward" type="data" format="tabular" multiple="True" label="UMI file" />
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diff changeset
87 <param name="reverse" type="data" format="fastq,fastq.gz" multiple="True" label="FASTQ reads" />
0
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
88 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
89 <when value="no">
4
01247aaf0a10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 94e4019f3e5e81d3a09cd92ce1e93587600847d8"
iuc
parents: 3
diff changeset
90 <param name="forward" type="data" format="fastq,fastq.gz" multiple="True" label="Forward reads" />
01247aaf0a10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 94e4019f3e5e81d3a09cd92ce1e93587600847d8"
iuc
parents: 3
diff changeset
91 <param name="reverse" type="data" format="fastq,fastq.gz" multiple="True" label="Reverse reads" />
0
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
92 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
93 </conditional>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
94 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
95 <when value="collection">
4
01247aaf0a10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 94e4019f3e5e81d3a09cd92ce1e93587600847d8"
iuc
parents: 3
diff changeset
96 <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />
0
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
97 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
98 </conditional>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
99 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
100 </conditional>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
101 </inputs>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
102 <outputs>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
103 <data format="tabular" name="sample">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
104 <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
parents:
diff changeset
105 </data>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
106 </outputs>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
107 <tests>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
108 <test>
2
1c75aa5de15e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 0
diff changeset
109 <param name="reference_transcriptome_source" value="history" />
0
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
110 <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
111 <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
112 <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
113 <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
114 <param name="forward" ftype="tabular" value="mm10_chrM.umi" />
4
01247aaf0a10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 94e4019f3e5e81d3a09cd92ce1e93587600847d8"
iuc
parents: 3
diff changeset
115 <param name="reverse" ftype="fastq.gz" value="mm10_chrM-1.r.fq.gz" />
0
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
116 <output name="sample">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
117 <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
parents:
diff changeset
118 <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
parents:
diff changeset
119 <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
parents:
diff changeset
120 </output>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
121 </test>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
122 <test>
2
1c75aa5de15e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 0
diff changeset
123 <param name="reference_transcriptome_source" value="history" />
0
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
124 <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
125 <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
126 <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
127 <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
128 <param name="reads">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
129 <collection type="paired">
4
01247aaf0a10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 94e4019f3e5e81d3a09cd92ce1e93587600847d8"
iuc
parents: 3
diff changeset
130 <element name="forward" value="mm10_chrM-1.f.fq.gz" ftype="fastq.gz"/>
01247aaf0a10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 94e4019f3e5e81d3a09cd92ce1e93587600847d8"
iuc
parents: 3
diff changeset
131 <element name="reverse" value="mm10_chrM-1.r.fq.gz" ftype="fastq.gz"/>
0
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
132 </collection>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
133 </param>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
134 <output name="sample">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
135 <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
136 <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
parents:
diff changeset
137 </output>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
138 </test>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
139 <test>
2
1c75aa5de15e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 0
diff changeset
140 <param name="reference_transcriptome_source" value="history" />
0
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
141 <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
142 <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
parents:
diff changeset
143 <param name="collection_selector" value="collection" />
4
01247aaf0a10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 94e4019f3e5e81d3a09cd92ce1e93587600847d8"
iuc
parents: 3
diff changeset
144 <param name="reads" ftype="fastq.gz" value="mm10_chrM-1.f.fq.gz" />
0
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
145 <output name="sample">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
146 <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
147 <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
iuc
parents:
diff changeset
148 </output>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
149 </test>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
150 <test>
2
1c75aa5de15e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 0
diff changeset
151 <param name="reference_transcriptome_source" value="history" />
0
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="felCat8_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="datasets" />
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="forward" ftype="fastq" value="felCat8_chrM_F.fq" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
157 <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
158 <output name="sample">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
159 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out4.tab" ftype="tabular" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
160 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out4.ec" ftype="tabular" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
161 </output>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
162 </test>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
163 <test>
2
1c75aa5de15e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 0
diff changeset
164 <param name="reference_transcriptome_source" value="cached" />
0
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
165 <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
166 <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
167 <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
168 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
169 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
170 <output name="sample">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
171 <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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172 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out6.ec" ftype="tabular" />
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173 <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out6.cells" ftype="tabular" />
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174 </output>
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175 </test>
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176 </tests>
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177 <help>
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178 <![CDATA[
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179 `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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180 ]]>
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181 </help>
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182 <expand macro="citations" />
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183 </tool>