Mercurial > repos > iuc > kallisto_pseudo
comparison kallisto_pseudo.xml @ 6:a157781cddd7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 168993a4e148506b1d3998c536caa2e501c36ccf
author | iuc |
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date | Wed, 31 May 2023 20:10:19 +0000 |
parents | 87c11c05d238 |
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5:87c11c05d238 | 6:a157781cddd7 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="kallisto_pseudo" name="Kallisto pseudo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> | 2 <tool id="kallisto_pseudo" name="Kallisto pseudo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> |
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 <xrefs> | |
8 <xref type="bio.tools">kallisto</xref> | |
9 </xrefs> | |
10 | |
7 <expand macro="requirements" /> | 11 <expand macro="requirements" /> |
8 <command detect_errors="exit_code"> | 12 <command detect_errors="exit_code"> |
9 <![CDATA[ | 13 <![CDATA[ |
10 #if $reference_transcriptome.reference_transcriptome_source == "history": | 14 #if $reference_transcriptome.reference_transcriptome_source == "history": |
11 ln -s '$reference_transcriptome.reference' reference.fa && | 15 ln -s '$reference_transcriptome.reference' reference.fa && |
65 <option value="single" selected="true">Single-end</option> | 69 <option value="single" selected="true">Single-end</option> |
66 <option value="paired">Paired</option> | 70 <option value="paired">Paired</option> |
67 </param> | 71 </param> |
68 <when value="single"> | 72 <when value="single"> |
69 <param name="reads" type="data" format="fastq,fastq.gz" multiple="True" label="Reads in FASTQ format" /> | 73 <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" /> | 74 <param 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" /> | 75 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" /> |
72 </when> | 76 </when> |
73 <when value="paired"> | 77 <when value="paired"> |
74 <conditional name="collection"> | 78 <conditional name="collection"> |
75 <param name="collection_selector" type="select" label="Collection or individual datasets"> | 79 <param name="collection_selector" type="select" label="Collection or individual datasets"> |
163 <test> | 167 <test> |
164 <param name="reference_transcriptome_source" value="cached" /> | 168 <param name="reference_transcriptome_source" value="cached" /> |
165 <param name="single_paired_selector" value="paired" /> | 169 <param name="single_paired_selector" value="paired" /> |
166 <param name="collection_selector" value="datasets" /> | 170 <param name="collection_selector" value="datasets" /> |
167 <param name="umi" value="yes" /> | 171 <param name="umi" value="yes" /> |
168 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" /> | 172 <param name="forward" ftype="tabular" dbkey="sacCer2" value="sacCer2_chrM.umi" /> |
169 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> | 173 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> |
170 <output name="sample"> | 174 <output name="sample"> |
171 <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" /> | 175 <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" /> |
172 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out6.ec" ftype="tabular" /> | 176 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out6.ec" ftype="tabular" /> |
173 <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out6.cells" ftype="tabular" /> | 177 <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out6.cells" ftype="tabular" /> |