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comparison 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
comparison
equal deleted inserted replaced
3:5ae5c312d718 4:01247aaf0a10
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.1"> 2 <tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.2">
3 <description>- run pseudoalignment on RNA-Seq transcripts</description> 3 <description>- run pseudoalignment on RNA-Seq transcripts</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
64 <param name="single_paired_selector" type="select" label="Single-end or paired reads"> 64 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
65 <option value="single" selected="true">Single-end</option> 65 <option value="single" selected="true">Single-end</option>
66 <option value="paired">Paired</option> 66 <option value="paired">Paired</option>
67 </param> 67 </param>
68 <when value="single"> 68 <when value="single">
69 <param name="reads" type="data" format="fastq" multiple="True" label="Reads in FASTQ format" /> 69 <param name="reads" type="data" format="fastq,fastq.gz" multiple="True" label="Reads in FASTQ format" />
70 <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" /> 70 <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" />
71 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" /> 71 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
72 </when> 72 </when>
73 <when value="paired"> 73 <when value="paired">
74 <conditional name="collection"> 74 <conditional name="collection">
82 <option value="no" selected="true">Paired FASTQ</option> 82 <option value="no" selected="true">Paired FASTQ</option>
83 <option value="yes">UMI</option> 83 <option value="yes">UMI</option>
84 </param> 84 </param>
85 <when value="yes"> 85 <when value="yes">
86 <param name="forward" type="data" format="tabular" multiple="True" label="UMI file" /> 86 <param name="forward" type="data" format="tabular" multiple="True" label="UMI file" />
87 <param name="reverse" type="data" format="fastq" multiple="True" label="FASTQ reads" /> 87 <param name="reverse" type="data" format="fastq,fastq.gz" multiple="True" label="FASTQ reads" />
88 </when> 88 </when>
89 <when value="no"> 89 <when value="no">
90 <param name="forward" type="data" format="fastq" multiple="True" label="Forward reads" /> 90 <param name="forward" type="data" format="fastq,fastq.gz" multiple="True" label="Forward reads" />
91 <param name="reverse" type="data" format="fastq" multiple="True" label="Reverse reads" /> 91 <param name="reverse" type="data" format="fastq,fastq.gz" multiple="True" label="Reverse reads" />
92 </when> 92 </when>
93 </conditional> 93 </conditional>
94 </when> 94 </when>
95 <when value="collection"> 95 <when value="collection">
96 <param name="reads" type="data_collection" format="fastq" collection_type="paired" label="Collection of reads" /> 96 <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />
97 </when> 97 </when>
98 </conditional> 98 </conditional>
99 </when> 99 </when>
100 </conditional> 100 </conditional>
101 </inputs> 101 </inputs>
110 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> 110 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
111 <param name="single_paired_selector" value="paired" /> 111 <param name="single_paired_selector" value="paired" />
112 <param name="collection_selector" value="datasets" /> 112 <param name="collection_selector" value="datasets" />
113 <param name="umi" value="yes" /> 113 <param name="umi" value="yes" />
114 <param name="forward" ftype="tabular" value="mm10_chrM.umi" /> 114 <param name="forward" ftype="tabular" value="mm10_chrM.umi" />
115 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" /> 115 <param name="reverse" ftype="fastq.gz" value="mm10_chrM-1.r.fq.gz" />
116 <output name="sample"> 116 <output name="sample">
117 <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out1.tab" ftype="tabular" /> 117 <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out1.tab" ftype="tabular" />
118 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out1.ec" ftype="tabular" /> 118 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out1.ec" ftype="tabular" />
119 <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out1.cells" ftype="tabular" /> 119 <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out1.cells" ftype="tabular" />
120 </output> 120 </output>
125 <param name="single_paired_selector" value="paired" /> 125 <param name="single_paired_selector" value="paired" />
126 <param name="collection_selector" value="collection" /> 126 <param name="collection_selector" value="collection" />
127 <param name="umi" value="no" /> 127 <param name="umi" value="no" />
128 <param name="reads"> 128 <param name="reads">
129 <collection type="paired"> 129 <collection type="paired">
130 <element name="forward" value="mm10_chrM-1.f.fq" /> 130 <element name="forward" value="mm10_chrM-1.f.fq.gz" ftype="fastq.gz"/>
131 <element name="reverse" value="mm10_chrM-1.r.fq" /> 131 <element name="reverse" value="mm10_chrM-1.r.fq.gz" ftype="fastq.gz"/>
132 </collection> 132 </collection>
133 </param> 133 </param>
134 <output name="sample"> 134 <output name="sample">
135 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out2.tab" ftype="tabular" /> 135 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out2.tab" ftype="tabular" />
136 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out2.ec" ftype="tabular" /> 136 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out2.ec" ftype="tabular" />
139 <test> 139 <test>
140 <param name="reference_transcriptome_source" value="history" /> 140 <param name="reference_transcriptome_source" value="history" />
141 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> 141 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
142 <param name="single_paired_selector" value="single" /> 142 <param name="single_paired_selector" value="single" />
143 <param name="collection_selector" value="collection" /> 143 <param name="collection_selector" value="collection" />
144 <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" /> 144 <param name="reads" ftype="fastq.gz" value="mm10_chrM-1.f.fq.gz" />
145 <output name="sample"> 145 <output name="sample">
146 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out3.tab" ftype="tabular" /> 146 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out3.tab" ftype="tabular" />
147 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out3.ec" ftype="tabular" /> 147 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out3.ec" ftype="tabular" />
148 </output> 148 </output>
149 </test> 149 </test>