Mercurial > repos > pavanvidem > dexseq
changeset 21:45022897fb7d draft
Uploaded
author | pavanvidem |
---|---|
date | Thu, 03 Sep 2015 11:26:08 -0400 |
parents | 169c48f14f31 |
children | 71cb8c5ae8bd |
files | dexseq_count.xml tool_dependencies.xml |
diffstat | 2 files changed, 12 insertions(+), 9 deletions(-) [+] |
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--- a/dexseq_count.xml Thu Sep 03 05:40:06 2015 -0400 +++ b/dexseq_count.xml Thu Sep 03 11:26:08 2015 -0400 @@ -4,11 +4,11 @@ <requirement type="package" version="3.1.0">R</requirement> <requirement type="package" version="1.14.2">DEXSeq</requirement> </requirements> - <command> + <command interpreter="python"> #if $mode.mode_select == "prepare": - python $INSTALL_DIR/python_scripts/dexseq_prepare_annotation.py -r $aggregate $gtf $flattened_gtf_out + dexseq_prepare_annotation.py -r $aggregate $gtffile $flattened_gtf_out #elif $mode.mode_select == "count": - python $INSTALL_DIR/python_scripts/dexseq_count.py -f bam -p $paired -r $order -s $stranded $flattened_gtf_in $bamfile $counts_file + dexseq_count.py -f bam -p $paired -r $order -s $stranded $flattened_gtf_in $bamfile $counts_file #end if </command> <inputs> @@ -18,19 +18,19 @@ <option value="count">Count reads</option> </param> <when value="prepare"> - <param name="gtf" type="gtf" label="GTF file"/> + <param name="gtffile" type="data" format="gff" label="GTF file"/> <param name="aggregate" type="boolean" checked="True" truevalue="yes" falsevalue="no" label="Aggretare genes with exons?" help="Indicates whether two or more genes sharing an exon should be merged into an 'aggregate gene'. If 'no', the exons that can not be assiged to a single gene are ignored."/> </when> <when value="count"> - <param name="bamfile" type="bam" label="Input bam file"/> - <param name="flattened_gtf_in" type="gtf" label="DEXSeq compatible GTF file" help="Created by prepare mode"/> - <param name="paired" type="boolean" checked="False" truevalue="yes" falsevalue="no" label="Is libray paired end?"/> + <param name="bamfile" type="data" format="bam" label="Input bam file"/> + <param name="flattened_gtf_in" type="data" format="gff" label="DEXSeq compatible GTF file" help="Created by prepare mode"/> + <param name="paired" type="boolean" checked="True" truevalue="yes" falsevalue="no" label="Is libray paired end?"/> <param name="stranded" type="select" label="Is library strand specific?"> <option value="no">No</option> <option value="yes">Yes</option> <option value="reverse">Yes, but reverse</option> </param> - <param name="qual" type="integer" value="10" label="Skip all reads with alignment quality lower than the given minimum value"> + <param name="qual" type="integer" value="10" label="Skip all reads with alignment quality lower than the given minimum value"/> <param name="order" type="select" label="Sorting order of alignments" help="If you generated your alignments using tophat, they are by default position sorted. Ignored for single-end data"> <option value="pos">By position</option> <option value="name">By name</option> @@ -43,7 +43,7 @@ <data format="tabular" name="counts_file" label="DEXSeq count reads on ${on_string}"> <filter>(mode['mode_select'] == 'count')</filter> </data> - <data format="gtf" name="flattened_gtf_out" label="DEXSeq prepare annotation ${on_string}"> + <data format="gff" name="flattened_gtf_out" label="DEXSeq prepare annotation ${on_string}"> <filter>(mode['mode_select'] == 'prepare')</filter> </data> </outputs>
--- a/tool_dependencies.xml Thu Sep 03 05:40:06 2015 -0400 +++ b/tool_dependencies.xml Thu Sep 03 11:26:08 2015 -0400 @@ -80,6 +80,9 @@ <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/statmod_1.4.21.tar.gz</package> <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/DEXSeq_1.14.2.tar.gz</package> </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/DEXSeq/python_scripts/</environment_variable> + </action> </actions> </install> <readme>