Mercurial > repos > iuc > kallisto_pseudo
diff kallisto_pseudo.xml @ 6:a157781cddd7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 168993a4e148506b1d3998c536caa2e501c36ccf
| author | iuc |
|---|---|
| date | Wed, 31 May 2023 20:10:19 +0000 |
| parents | 87c11c05d238 |
| children |
line wrap: on
line diff
--- a/kallisto_pseudo.xml Sun Jul 18 17:53:43 2021 +0000 +++ b/kallisto_pseudo.xml Wed May 31 20:10:19 2023 +0000 @@ -1,9 +1,13 @@ <?xml version="1.0"?> <tool id="kallisto_pseudo" name="Kallisto pseudo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> - <description>- run pseudoalignment on RNA-Seq transcripts</description> + <description>run pseudoalignment on RNA-Seq transcripts</description> <macros> <import>macros.xml</import> </macros> + <xrefs> + <xref type="bio.tools">kallisto</xref> + </xrefs> + <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ @@ -67,7 +71,7 @@ </param> <when value="single"> <param name="reads" type="data" format="fastq,fastq.gz" multiple="True" label="Reads in FASTQ format" /> - <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" /> + <param argument="--fragment-length" type="integer" value="200" label="Average fragment length" /> <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" /> </when> <when value="paired"> @@ -165,7 +169,7 @@ <param name="single_paired_selector" value="paired" /> <param name="collection_selector" value="datasets" /> <param name="umi" value="yes" /> - <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" /> + <param name="forward" ftype="tabular" dbkey="sacCer2" value="sacCer2_chrM.umi" /> <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> <output name="sample"> <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" />