Mercurial > repos > iuc > kallisto_pseudo
changeset 2:1c75aa5de15e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
| author | iuc |
|---|---|
| date | Sat, 09 Dec 2017 05:34:01 -0500 |
| parents | 63f76b9f4ba7 |
| children | 5ae5c312d718 |
| files | kallisto_pseudo.xml macros.xml |
| diffstat | 2 files changed, 30 insertions(+), 27 deletions(-) [+] |
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--- a/kallisto_pseudo.xml Tue Sep 05 03:25:54 2017 -0400 +++ b/kallisto_pseudo.xml Sat Dec 09 05:34:01 2017 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.0"> +<tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.1"> <description>- run pseudoalignment on RNA-Seq transcripts</description> <macros> <import>macros.xml</import> @@ -7,12 +7,12 @@ <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ - #if $reference_genome.reference_genome_source == "history": - ln -s '$reference_genome.reference' reference.fa && + #if $reference_transcriptome.reference_transcriptome_source == "history": + ln -s '$reference_transcriptome.reference' reference.fa && kallisto index reference.fa -i reference.kallisto && #set index_path = 'reference.kallisto' #else: - #set index_path = $reference_genome.index.fields.path + #set index_path = $reference_transcriptome.index.fields.path #end if kallisto pseudo -i '$index_path' #if $pseudobam: @@ -67,23 +67,7 @@ </configfile> </configfiles> <inputs> - <conditional name="reference_genome"> - <param name="reference_genome_source" type="select" label="Reference genome for pseudoalignment"> - <option value="indexed" selected="true">Use a built-in genome</option> - <option value="history">Use a genome from history</option> - </param> - <when value="indexed"> - <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy administrator"> - <options from_data_table="kallisto_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No genomes are available for the selected input dataset" /> - </options> - </param> - </when> - <when value="history"> - <param name="reference" type="data" format="fasta" label="FASTA reference genome" /> - </when> - </conditional> + <expand macro="reference_input" /> <conditional name="single_paired"> <param name="single_paired_selector" type="select" label="Single-end or paired reads"> <option value="single" selected="true">Single-end</option> @@ -134,7 +118,7 @@ </outputs> <tests> <test> - <param name="reference_genome_source" value="history" /> + <param name="reference_transcriptome_source" value="history" /> <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> <param name="single_paired_selector" value="paired" /> <param name="collection_selector" value="datasets" /> @@ -148,7 +132,7 @@ </output> </test> <test> - <param name="reference_genome_source" value="history" /> + <param name="reference_transcriptome_source" value="history" /> <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> <param name="single_paired_selector" value="paired" /> <param name="collection_selector" value="collection" /> @@ -165,7 +149,7 @@ </output> </test> <test> - <param name="reference_genome_source" value="history" /> + <param name="reference_transcriptome_source" value="history" /> <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> <param name="single_paired_selector" value="single" /> <param name="collection_selector" value="collection" /> @@ -176,7 +160,7 @@ </output> </test> <test> - <param name="reference_genome_source" value="history" /> + <param name="reference_transcriptome_source" value="history" /> <param name="reference" ftype="fasta" value="felCat8_chrM.fa" /> <param name="single_paired_selector" value="paired" /> <param name="collection_selector" value="datasets" /> @@ -189,7 +173,7 @@ </output> </test> <test> - <param name="reference_genome_source" value="cached" /> + <param name="reference_transcriptome_source" value="cached" /> <param name="single_paired_selector" value="paired" /> <param name="collection_selector" value="datasets" /> <param name="pseudobam" value="true" /> @@ -202,7 +186,7 @@ <output name="pseudobam_output" file="kallisto_pseudo_out5.bam" ftype="bam" /> </test> <test> - <param name="reference_genome_source" value="cached" /> + <param name="reference_transcriptome_source" value="cached" /> <param name="single_paired_selector" value="paired" /> <param name="collection_selector" value="datasets" /> <param name="umi" value="yes" />
--- a/macros.xml Tue Sep 05 03:25:54 2017 -0400 +++ b/macros.xml Sat Dec 09 05:34:01 2017 -0500 @@ -12,4 +12,23 @@ <citation type="doi">doi:10.1038/nbt.3519</citation> </citations> </xml> + <xml name="reference_input"> + <conditional name="reference_transcriptome"> + <param name="reference_transcriptome_source" type="select" label="Reference transcriptome for quantification"> + <option value="indexed" selected="true">Use a built-in transcriptome</option> + <option value="history">Use a transcriptome from history</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy administrator"> + <options from_data_table="kallisto_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No transcriptomes are available for the selected input dataset" /> + </options> + </param> + </when> + <when value="history"> + <param name="reference" type="data" format="fasta" label="FASTA reference transcriptome" /> + </when> + </conditional> + </xml> </macros> \ No newline at end of file