Mercurial > repos > iuc > kallisto_pseudo

annotate kallisto_pseudo.xml @ 7:ce5d418183c5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f173f58bc695c22364685c2ffbb9f3e95708f00f
author iuc
date Mon, 05 Jun 2023 22:06:13 +0000
parents a157781cddd7
children
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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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2 <tool id="kallisto_pseudo" name="Kallisto pseudo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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3 <description>run pseudoalignment on RNA-Seq transcripts</description>
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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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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>
6
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7 <xrefs>
a157781cddd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 168993a4e148506b1d3998c536caa2e501c36ccf
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8 <xref type="bio.tools">kallisto</xref>
a157781cddd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 168993a4e148506b1d3998c536caa2e501c36ccf
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9 </xrefs>
a157781cddd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 168993a4e148506b1d3998c536caa2e501c36ccf
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10
0
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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11 <expand macro="requirements" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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12 <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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13 <![CDATA[
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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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14 #if $reference_transcriptome.reference_transcriptome_source == "history":
1c75aa5de15e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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15 ln -s '$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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16 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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17 #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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18 #else:
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19 #set index_path = $reference_transcriptome.index.fields.path
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20 #end if
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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21 kallisto pseudo -i '$index_path'
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22 --threads \${GALAXY_SLOTS:-1}
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23 -o .
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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 #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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26 --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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27 --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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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($single_paired.collection.collection_selector) == 'collection':
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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30 '$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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31 '$single_paired.collection.reads.reverse'
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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32 #else:
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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33 #if str($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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34 --batch '$batch' --umi
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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35 #else:
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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36 '$single_paired.collection.fastq_umi.forward'
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37 '$single_paired.collection.fastq_umi.reverse'
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38 #end if
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
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41 && 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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42 mkdir outputs &&
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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43 if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi &&
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44 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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45 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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46 if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi &&
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47 if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi
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48 ]]>
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49 </command>
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50 <configfiles>
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51 <configfile name="batch">
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52 <![CDATA[
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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53 #if str($single_paired.single_paired_selector) == 'single':
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54 cell1 $single_paired.reads
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55 #else:
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56 #if str($single_paired.collection.collection_selector) == 'collection':
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57 cell1 $single_paired.collection.reads.forward $single_paired.collection.reads.reverse
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58 #else:
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59 cell1 $single_paired.collection.fastq_umi.forward $single_paired.collection.fastq_umi.reverse
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60 #end if
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61 #end if
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62 ]]>
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63 </configfile>
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64 </configfiles>
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65 <inputs>
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66 <expand macro="reference_input" />
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67 <conditional name="single_paired">
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68 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
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69 <option value="single" selected="true">Single-end</option>
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70 <option value="paired">Paired</option>
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71 </param>
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72 <when value="single">
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73 <param name="reads" type="data" format="fastq,fastq.gz" multiple="True" label="Reads in FASTQ format" />
6
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74 <param argument="--fragment-length" type="integer" value="200" label="Average fragment length" />
0
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75 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
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76 </when>
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77 <when value="paired">
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78 <conditional name="collection">
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79 <param name="collection_selector" type="select" label="Collection or individual datasets">
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80 <option value="datasets" selected="true">Individual files</option>
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81 <option value="collection">Pair or list of pairs</option>
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82 </param>
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83 <when value="datasets">
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84 <conditional name="fastq_umi">
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85 <param name="umi" type="select" label="Pseudoalignment uses UMIs">
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86 <option value="no" selected="true">Paired FASTQ</option>
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87 <option value="yes">UMI</option>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
88 </param>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
89 <when value="yes">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
90 <param name="forward" type="data" format="tabular" multiple="True" label="UMI file" />
4
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="FASTQ 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 <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
94 <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
95 <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
96 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
97 </conditional>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
98 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
99 <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
100 <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
101 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
102 </conditional>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
103 </when>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
104 </conditional>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
105 </inputs>
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 <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
108 <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
109 </data>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
110 </outputs>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
111 <tests>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
112 <test>
2
1c75aa5de15e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 0
diff changeset
113 <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
114 <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
115 <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
116 <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
117 <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
118 <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
119 <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
120 <output name="sample">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
121 <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
122 <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
123 <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
124 </output>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
125 </test>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
126 <test>
2
1c75aa5de15e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 0
diff changeset
127 <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
128 <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
129 <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
130 <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
131 <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
132 <param name="reads">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
133 <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
134 <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
135 <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
136 </collection>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
137 </param>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
138 <output name="sample">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
139 <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
140 <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
141 </output>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
142 </test>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
143 <test>
2
1c75aa5de15e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 0
diff changeset
144 <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
145 <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
146 <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
147 <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
148 <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
149 <output name="sample">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
150 <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
151 <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
152 </output>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
153 </test>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
154 <test>
2
1c75aa5de15e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 0
diff changeset
155 <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
156 <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
157 <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
158 <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
159 <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
160 <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
161 <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
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_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
164 <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
165 </output>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
166 </test>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff changeset
167 <test>
2
1c75aa5de15e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 0
diff changeset
168 <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
169 <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
170 <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
171 <param name="umi" value="yes" />
6
a157781cddd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 168993a4e148506b1d3998c536caa2e501c36ccf
iuc
parents: 5
diff changeset
172 <param name="forward" ftype="tabular" dbkey="sacCer2" value="sacCer2_chrM.umi" />
0
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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173 <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
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174 <output name="sample">
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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175 <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
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176 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out6.ec" ftype="tabular" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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177 <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out6.cells" ftype="tabular" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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178 </output>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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179 </test>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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180 </tests>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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181 <help>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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182 <![CDATA[
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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183 `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.
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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184 ]]>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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185 </help>
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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186 <expand macro="citations" />
2953303df011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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187 </tool>