Mercurial > repos > yhoogstrate > crossmap
diff crossmap.xml @ 11:a5eb1023fc34 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
| author | yhoogstrate |
|---|---|
| date | Wed, 05 Aug 2015 03:53:14 -0400 |
| parents | 0cae6e3273a8 |
| children | 7e32d2a88c07 |
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--- a/crossmap.xml Wed Aug 05 03:11:38 2015 -0400 +++ b/crossmap.xml Wed Aug 05 03:53:14 2015 -0400 @@ -6,7 +6,7 @@ </requirements> <stdio> - <regex match="Usage: CrossMap.py" source="stdin" level="fatal"/> + <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/> <regex match=".*" source="both" level="log" description="tool progress"/> </stdio> @@ -35,10 +35,11 @@ "$multiple.seq_source.input_fasta" #end if - <!-- BED format does not write to the output file, but does write fails to stdout --> - > "$output" + #if $multiple.include_fails == "true" + > + #end if - 2>/dev/null + "$output" </command> <inputs> @@ -73,7 +74,7 @@ </when> <when value="history"> <param type="data" format="bam,sam" name="input" label="BAM/SAM file" /> - <param type="data" name="input_chain" label="LiftOver chain file" /> + <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> </when> </conditional> @@ -105,9 +106,10 @@ </when> <when value="history"> <param type="data" format="bed" name="input" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." /> - <param type="data" name="input_chain" label="LiftOver chain file" /> + <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> </when> </conditional> + <param name="include_fails" type="boolean" truevalue="true" falsevalue="false" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')" /> </when> <when value="bigwig"> <conditional name="seq_source"> @@ -130,8 +132,8 @@ </param> </when> <when value="history"> - <param format="bigwig" name="input" type="data" label="BigWig file" /> - <param type="data" name="input_chain" label="LiftOver chain file" /> + <param type="data" format="bigwig" name="input" label="BigWig file" /> + <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> </when> </conditional> </when> @@ -156,8 +158,8 @@ </param> </when> <when value="history"> - <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file" /> - <param type="data" name="input_chain" label="LiftOver chain file" /> + <param type="data" format="gtf,gff,gff3" name="input" label="GTF/GFF file" /> + <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> </when> </conditional> </when> @@ -199,7 +201,7 @@ <validator type="unspecified_build" /> <validator type="dataset_metadata_in_file" filename="all_fasta.loc" metadata_name="dbkey" metadata_column="1" message="LiftOver mapping (FASTA file) is not available for the specified build." /> </param> - <param type="data" name="input_chain" multiple="false" label="LiftOver chain file" /> + <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" /> <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file"> <options from_file="all_fasta.loc"> <column name="name" index="2"/> @@ -211,8 +213,8 @@ <when value="history_all"> <param type="data" format="vcf" name="input" label="VCF file" /> - <param type="data" name="input_all_chain" multiple="false" label="LiftOver chain file" /> - <param type="data" format="fasta" name="input_all_fasta" multiple="false" label="Full genome FASTA file" /> + <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" /> + <param type="data" format="fasta" name="input_fasta" multiple="false" label="Full genome FASTA file" /> </when> </conditional> </when> @@ -238,7 +240,7 @@ </when> <when value="history"> <param format="wig" name="input" type="data" label="Wiggle file" /> - <param type="data" name="input_chain" label="LiftOver chain file" /> + <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> </when> </conditional> </when> @@ -251,10 +253,41 @@ <tests> <test> - <param name="input" value="test1.hg19.txt"/> - <param name="input" value="hg18tohg19.chain"/> - <output name="output" file="test1.hg18.txt"/> + <param name="input_format" value="bed"/> + <param name="index_source" value="history"/> + <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/> + <param name="input_chain" value="aToB.over.chain" ftype="txt"/> + <param name="include_fails" value="false"/> + + <output name="output" file="test_bed_01_output_a__only-matches.bed"/> + </test> + <!--<test> + <param name="input_format" value="bed"/> + <param name="index_source" value="history"/> + <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/> + <param name="input_chain" value="aToB.over.chain" ftype="txt"/> + <param name="include_fails" value="true"/> + + <output name="output" file="test_bed_02_output_a__all.bed"/> </test> + <test> + <param name="input_format" value="bed"/> + <param name="index_source" value="history"/> + <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/> + <param name="input_chain" value="aToB.over.chain" ftype="txt"/> + <param name="include_fails" value="false"/> + + <output name="output" file="test_bed_02_output_a__only-matches.bed"/> + </test> + <test> + <param name="input_format" value="bed"/> + <param name="index_source" value="history"/> + <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/> + <param name="input_chain" value="aToB.over.chain" ftype="txt"/> + <param name="include_fails" value="true"/> + + <output name="output" file="test_bed_02_output_a__all.bed"/> + </test>--> </tests> <help> @@ -267,7 +300,6 @@ ------------ BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns. BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 - </help> <citations>