Mercurial > repos > iuc > chira_extract
diff chira_extract.xml @ 5:dea6bc47a47e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
author | iuc |
---|---|
date | Fri, 20 Mar 2020 05:04:28 -0400 |
parents | 061844f6837f |
children | 56b2d956a1a6 |
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--- a/chira_extract.xml Thu Mar 12 17:05:26 2020 -0400 +++ b/chira_extract.xml Fri Mar 20 05:04:28 2020 -0400 @@ -25,11 +25,11 @@ -sc '$score_cutoff' -co '$chimeric_overlap' #if str($reference.ref_type) == "single": - -f1 '$ref_fasta' + -f1 '$reference.ref_fasta' #else if str($reference.ref_type) == "split": - -f1 '$ref_fasta1' - -f2 '$ref_fasta2' - #end if + -f1 '$reference.ref_fasta1' + -f2 '$reference.ref_fasta2' + #end if $hybridize -p "\${GALAXY_SLOTS:-2}" -o ./ @@ -62,7 +62,7 @@ </when> <when value="no"> <!-- Do nothing --> - </when> + </when> </conditional> <param name="tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max="1" help="Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]"/> @@ -88,12 +88,12 @@ </conditional> <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" /> </inputs> - + <outputs> <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/> <data format="tabular" name="singletons" from_work_dir="singletons" label="ChiRA singleton reads on ${on_string}"/> </outputs> - + <tests> <test expect_num_outputs="2"> <param name="loci" value="loci.counts"/> @@ -112,7 +112,7 @@ **What it does** -This tool extracts the best chimeric alignments for each read. User can optionally hybridize the loci where the chimeric arms are mapping to. +This tool extracts the best chimeric alignments for each read. User can optionally hybridize the loci where the chimeric arms are mapping to. **Inputs**