Mercurial > repos > iuc > kallisto_pseudo
diff kallisto_pseudo.xml @ 4:01247aaf0a10 draft
"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 |
line wrap: on
line diff
--- a/kallisto_pseudo.xml Thu Sep 26 09:11:24 2019 -0400 +++ b/kallisto_pseudo.xml Tue Apr 06 21:08:39 2021 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.1"> +<tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.2"> <description>- run pseudoalignment on RNA-Seq transcripts</description> <macros> <import>macros.xml</import> @@ -66,7 +66,7 @@ <option value="paired">Paired</option> </param> <when value="single"> - <param name="reads" type="data" format="fastq" multiple="True" label="Reads in FASTQ format" /> + <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="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" /> </when> @@ -84,16 +84,16 @@ </param> <when value="yes"> <param name="forward" type="data" format="tabular" multiple="True" label="UMI file" /> - <param name="reverse" type="data" format="fastq" multiple="True" label="FASTQ reads" /> + <param name="reverse" type="data" format="fastq,fastq.gz" multiple="True" label="FASTQ reads" /> </when> <when value="no"> - <param name="forward" type="data" format="fastq" multiple="True" label="Forward reads" /> - <param name="reverse" type="data" format="fastq" multiple="True" label="Reverse reads" /> + <param name="forward" type="data" format="fastq,fastq.gz" multiple="True" label="Forward reads" /> + <param name="reverse" type="data" format="fastq,fastq.gz" multiple="True" label="Reverse reads" /> </when> </conditional> </when> <when value="collection"> - <param name="reads" type="data_collection" format="fastq" collection_type="paired" label="Collection of reads" /> + <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" /> </when> </conditional> </when> @@ -112,7 +112,7 @@ <param name="collection_selector" value="datasets" /> <param name="umi" value="yes" /> <param name="forward" ftype="tabular" value="mm10_chrM.umi" /> - <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" /> + <param name="reverse" ftype="fastq.gz" value="mm10_chrM-1.r.fq.gz" /> <output name="sample"> <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out1.tab" ftype="tabular" /> <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out1.ec" ftype="tabular" /> @@ -127,8 +127,8 @@ <param name="umi" value="no" /> <param name="reads"> <collection type="paired"> - <element name="forward" value="mm10_chrM-1.f.fq" /> - <element name="reverse" value="mm10_chrM-1.r.fq" /> + <element name="forward" value="mm10_chrM-1.f.fq.gz" ftype="fastq.gz"/> + <element name="reverse" value="mm10_chrM-1.r.fq.gz" ftype="fastq.gz"/> </collection> </param> <output name="sample"> @@ -141,7 +141,7 @@ <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> <param name="single_paired_selector" value="single" /> <param name="collection_selector" value="collection" /> - <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" /> + <param name="reads" ftype="fastq.gz" value="mm10_chrM-1.f.fq.gz" /> <output name="sample"> <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out3.tab" ftype="tabular" /> <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out3.ec" ftype="tabular" />