Mercurial > repos > yhoogstrate > crossmap
changeset 30:179bf64d12ef draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
| author | yhoogstrate |
|---|---|
| date | Thu, 12 Nov 2015 10:26:25 -0500 |
| parents | 871455bebf64 |
| children | ebcd672e9072 |
| files | crossmap.xml |
| diffstat | 1 files changed, 240 insertions(+), 242 deletions(-) [+] |
line wrap: on
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--- a/crossmap.xml Thu Nov 12 10:13:37 2015 -0500 +++ b/crossmap.xml Thu Nov 12 10:26:25 2015 -0500 @@ -16,270 +16,127 @@ <command><!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: --> python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py - ${multiple.input_format.replace("sam","bam")} + ${input_format.replace("sam","bam")} - #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached" + #if $input_format == "vcf" and $seq_source.index_source == "cached" <!-- This is the 2nd dbkey, and the corresponding value has to be looked up --> - "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }" + "${filter(lambda x: str( x[1] ) == str($seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }" #else - "$multiple.seq_source.input_chain" + "$seq_source.input_chain" #end if - #if $multiple.input_format in ["bam", "sam"] - -m $multiple.insert_size - -s $multiple.insert_size_stdev - -t $multiple.insert_size_fold + #if $input_format in ["bam", "sam"] + -m $insert_size + -s $insert_size_stdev + -t $insert_size_fold #end if - "$multiple.seq_source.input" + "$seq_source.input" - #if $multiple.input_format == "vcf" - "$multiple.seq_source.input_fasta" + #if $input_format == "vcf" + "$seq_source.input_fasta" #end if - #if str($multiple.include_fails) == "True" + #if str($include_fails) == "True" > #end if "$output" - #if $multiple.input_format in ["bam", "sam"] - ; mv "${output}.${multiple.input_format}" "$output" - ; mv "${output}.unmap.${multiple.input_format}" "$output_unmapped" - #else if $multiple.input_format in ["vcf"] + #if $input_format in ["bam", "sam"] + ; mv "${output}.${input_format}" "$output" + ; mv "${output}.unmap.${input_format}" "$output_unmapped" + #else if $input_format in ["vcf"] ; mv "${output}" "$output" ; mv "${output}.unmap" "$output_unmapped" - #else if $multiple.input_format in ["wig", "bigwig"] + #else if $input_format in ["wig", "bigwig"] ; mv "${output}.bw" "$output" ; mv "${output}.sorted.bgr" "$output2" #end if </command> <inputs> - <conditional name="multiple"> - <param name="input_format" type="select" label="Convert a file of the following format"> - <option value="bam">BAM</option> - <option value="sam">SAM</option> - <option value="bed">BED or BED-like</option> - <option value="bigwig">BigWig</option> - <option value="gff">GFF or GTF</option> - <option value="vcf">VCF</option> - <option value="wig">Wiggle or bedGraph</option> - </param> - <when value="bam"> - <conditional name="seq_source"> - <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> - <option value="cached">Local data (in galaxy)</option> - <option value="history">From History</option> - </param> - <when value="cached"> - <param type="data" format="bam" name="input" label="BAM/SAM file"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> - </param> - <param name="input_chain" type="select" label="Lift Over To"> - <options from_file="liftOver.loc"> - <column name="name" index="1"/> - <column name="value" index="2"/> - <column name="dbkey" index="0"/> - <filter type="data_meta" ref="input" key="dbkey" column="0" /> - </options> - </param> - </when> - <when value="history"> - <param type="data" format="bam,sam" name="input" label="BAM/SAM file" /> - <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> - </when> - </conditional> - - <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" /> - <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" /> - <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" /> - - <param name="include_fails" type="hidden" tvalue="False" /> - </when> - <when value="sam"><!-- BAM and SAM are exactly the same conditions, but they need to be separate to get the proper output format --> - <conditional name="seq_source"> - <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> - <option value="cached">Local data (in galaxy)</option> - <option value="history">From History</option> - </param> - <when value="cached"> - <param type="data" format="sam" name="input" label="BAM/SAM file"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> - </param> - <param name="input_chain" type="select" label="Lift Over To"> - <options from_file="liftOver.loc"> - <column name="name" index="1"/> - <column name="value" index="2"/> - <column name="dbkey" index="0"/> - <filter type="data_meta" ref="input" key="dbkey" column="0" /> - </options> - </param> - </when> - <when value="history"> - <param type="data" format="bam,sam" name="input" label="BAM/SAM file" /> - <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> - </when> - </conditional> - - <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" /> - <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" /> - <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" /> - - <param name="include_fails" type="hidden" tvalue="False" /> - </when> - <when value="bed"> - <conditional name="seq_source"> - <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> - <option value="cached">Local data (in galaxy)</option> - <option value="history">From History</option> - </param> - <when value="cached"> - <param format="bed" name="input" type="data" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns."> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> - </param> - <param name="input_chain" type="select" label="Lift Over To"> - <options from_file="liftOver.loc"> - <column name="name" index="1"/> - <column name="value" index="2"/> - <column name="dbkey" index="0"/> - <filter type="data_meta" ref="input" key="dbkey" column="0" /> - </options> - </param> - </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" format="csv" name="input_chain" label="LiftOver chain file" /> - </when> - </conditional> - - <param name="include_fails" type="boolean" truevalue="True" checked="false" 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"> - <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> - <option value="cached">Local data (in galaxy)</option> - <option value="history">From History</option> - </param> - <when value="cached"> - <param format="bigwig" name="input" type="data" label="BigWig file"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> - </param> - <param name="input_chain" type="select" label="Lift Over To"> - <options from_file="liftOver.loc"> - <column name="name" index="1"/> - <column name="value" index="2"/> - <column name="dbkey" index="0"/> - <filter type="data_meta" ref="input" key="dbkey" column="0" /> - </options> - </param> - </when> - <when value="history"> - <param type="data" format="bigwig" name="input" label="BigWig file" /> - <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> - </when> - </conditional> - - <param name="include_fails" type="hidden" tvalue="False" /> - </when> - <when value="gff"> - <conditional name="seq_source"> - <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> - <option value="cached">Local data (in galaxy)</option> - <option value="history">From History</option> - </param> - <when value="cached"> - <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> - </param> - <param name="input_chain" type="select" label="Lift Over To"> - <options from_file="liftOver.loc"> - <column name="name" index="1"/> - <column name="value" index="2"/> - <column name="dbkey" index="0"/> - <filter type="data_meta" ref="input" key="dbkey" column="0" /> - </options> - </param> - </when> - <when value="history"> - <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> - - <param name="include_fails" type="boolean" truevalue="True" checked="false" 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="vcf"> - <conditional name="seq_source"> - <param name="index_source" type="select" label="Source for LiftOver Data"> - <option value="cached">Local data (in galaxy)</option> - <option value="history_chain">Chain file from History</option> - <option value="history_all">Chain & FASTA files from History</option> - </param> - + <param name="input_format" type="select" label="Convert a file of the following format"> + <option value="bam">BAM</option> + <option value="sam">SAM</option> + <option value="bed">BED or BED-like</option> + <option value="bigwig">BigWig</option> + <option value="gff">GFF or GTF</option> + <option value="vcf">VCF</option> + <option value="wig">Wiggle or bedGraph</option> + </param> + <when value="bam"> + <conditional name="seq_source"> + <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> + <option value="cached">Local data (in galaxy)</option> + <option value="history">From History</option> + </param> <when value="cached"> - <param type="data" format="vcf" name="input" label="VCF file"> + <param type="data" format="bam" name="input" label="BAM/SAM file"> <validator type="unspecified_build" /> <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> </param> - - <!-- automatically fetch a FASTA file from the same DBKEY as the chain file --> - <param name="input_chain" type="select" label="Lift Over To (Chain file)"> + <param name="input_chain" type="select" label="Lift Over To"> <options from_file="liftOver.loc"> - <column name="name" index="1" /> - <column name="value" index="1" /><!-- It is not possible to send the *.chain file as value, and obtain the 2nd dbkey as parameter via a filter --> - <column name="dbkey" index="0" /> + <column name="name" index="1"/> + <column name="value" index="2"/> + <column name="dbkey" index="0"/> <filter type="data_meta" ref="input" key="dbkey" column="0" /> </options> </param> - - <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"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> - <filter type="param_value" ref="input_chain" column="1" /> - </options> - </param> </when> - - <when value="history_chain"> - <param type="data" format="vcf" name="input" label="VCF file"> + <when value="history"> + <param type="data" format="bam,sam" name="input" label="BAM/SAM file" /> + <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> + </when> + </conditional> + + <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" /> + <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" /> + <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" /> + + <param name="include_fails" type="hidden" tvalue="False" /> + </when> + <when value="sam"><!-- BAM and SAM are exactly the same conditions, but they need to be separate to get the proper output format --> + <conditional name="seq_source"> + <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> + <option value="cached">Local data (in galaxy)</option> + <option value="history">From History</option> + </param> + <when value="cached"> + <param type="data" format="sam" name="input" label="BAM/SAM file"> <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." /> + <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> </param> - <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"/> - <column name="value" index="3"/> - <column name="dbkey" index="1"/> + <param name="input_chain" type="select" label="Lift Over To"> + <options from_file="liftOver.loc"> + <column name="name" index="1"/> + <column name="value" index="2"/> + <column name="dbkey" index="0"/> + <filter type="data_meta" ref="input" key="dbkey" column="0" /> </options> </param> </when> - - <when value="history_all"> - <param type="data" format="vcf" name="input" label="VCF 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 value="history"> + <param type="data" format="bam,sam" name="input" label="BAM/SAM file" /> + <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> </when> - </conditional> - - <param name="include_fails" type="hidden" tvalue="False" /> - </when> - <when value="wig"> - <conditional name="seq_source"> - <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> - <option value="cached">Local data (in galaxy)</option> - <option value="history">From History</option> - </param> + </conditional> + + <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" /> + <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" /> + <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" /> + + <param name="include_fails" type="hidden" tvalue="False" /> + </when> + <when value="bed"> + <conditional name="seq_source"> + <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> + <option value="cached">Local data (in galaxy)</option> + <option value="history">From History</option> + </param> <when value="cached"> - <param format="wig" name="input" type="data" label="Wiggle file"> + <param format="bed" name="input" type="data" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns."> <validator type="unspecified_build" /> <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> </param> @@ -293,40 +150,181 @@ </param> </when> <when value="history"> - <param format="wig" name="input" type="data" label="Wiggle file" /> + <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" format="csv" name="input_chain" label="LiftOver chain file" /> </when> - </conditional> + </conditional> + + <param name="include_fails" type="boolean" truevalue="True" checked="false" 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"> + <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> + <option value="cached">Local data (in galaxy)</option> + <option value="history">From History</option> + </param> + <when value="cached"> + <param format="bigwig" name="input" type="data" label="BigWig file"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> + </param> + <param name="input_chain" type="select" label="Lift Over To"> + <options from_file="liftOver.loc"> + <column name="name" index="1"/> + <column name="value" index="2"/> + <column name="dbkey" index="0"/> + <filter type="data_meta" ref="input" key="dbkey" column="0" /> + </options> + </param> + </when> + <when value="history"> + <param type="data" format="bigwig" name="input" label="BigWig file" /> + <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> + </when> + </conditional> + + <param name="include_fails" type="hidden" tvalue="False" /> + </when> + <when value="gff"> + <conditional name="seq_source"> + <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> + <option value="cached">Local data (in galaxy)</option> + <option value="history">From History</option> + </param> + <when value="cached"> + <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> + </param> + <param name="input_chain" type="select" label="Lift Over To"> + <options from_file="liftOver.loc"> + <column name="name" index="1"/> + <column name="value" index="2"/> + <column name="dbkey" index="0"/> + <filter type="data_meta" ref="input" key="dbkey" column="0" /> + </options> + </param> + </when> + <when value="history"> + <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> + + <param name="include_fails" type="boolean" truevalue="True" checked="false" 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="vcf"> + <conditional name="seq_source"> + <param name="index_source" type="select" label="Source for LiftOver Data"> + <option value="cached">Local data (in galaxy)</option> + <option value="history_chain">Chain file from History</option> + <option value="history_all">Chain & FASTA files from History</option> + </param> - <param name="include_fails" type="hidden" tvalue="False" /> - </when> - </conditional> + <when value="cached"> + <param type="data" format="vcf" name="input" label="VCF file"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> + </param> + + <!-- automatically fetch a FASTA file from the same DBKEY as the chain file --> + <param name="input_chain" type="select" label="Lift Over To (Chain file)"> + <options from_file="liftOver.loc"> + <column name="name" index="1" /> + <column name="value" index="1" /><!-- It is not possible to send the *.chain file as value, and obtain the 2nd dbkey as parameter via a filter --> + <column name="dbkey" index="0" /> + <filter type="data_meta" ref="input" key="dbkey" column="0" /> + </options> + </param> + + <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"/> + <column name="value" index="3"/> + <column name="dbkey" index="1"/> + <filter type="param_value" ref="input_chain" column="1" /> + </options> + </param> + </when> + + <when value="history_chain"> + <param type="data" format="vcf" name="input" label="VCF file"> + <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" 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"/> + <column name="value" index="3"/> + <column name="dbkey" index="1"/> + </options> + </param> + </when> + + <when value="history_all"> + <param type="data" format="vcf" name="input" label="VCF 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> + + <param name="include_fails" type="hidden" tvalue="False" /> + </when> + <when value="wig"> + <conditional name="seq_source"> + <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> + <option value="cached">Local data (in galaxy)</option> + <option value="history">From History</option> + </param> + <when value="cached"> + <param format="wig" name="input" type="data" label="Wiggle file"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> + </param> + <param name="input_chain" type="select" label="Lift Over To"> + <options from_file="liftOver.loc"> + <column name="name" index="1"/> + <column name="value" index="2"/> + <column name="dbkey" index="0"/> + <filter type="data_meta" ref="input" key="dbkey" column="0" /> + </options> + </param> + </when> + <when value="history"> + <param format="wig" name="input" type="data" label="Wiggle file" /> + <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> + </when> + </conditional> + + <param name="include_fails" type="hidden" tvalue="False" /> + </when> </inputs> <outputs> <data format="text" name="output" label="${tool.name} on ${on_string}"> <change_format> - <when input="multiple.input_format" value="bam" format="bam" /> - <when input="multiple.input_format" value="sam" format="sam" /> - <when input="multiple.input_format" value="bed" format="bed" /> - <when input="multiple.input_format" value="bigwig" format="bigwig" /> - <when input="multiple.input_format" value="gff" format="gff" /> - <when input="multiple.input_format" value="vcf" format="vcf" /> - <when input="imultiple.nput_format" value="wig" format="bigwig" /> + <when input="input_format" value="bam" format="bam" /> + <when input="input_format" value="sam" format="sam" /> + <when input="input_format" value="bed" format="bed" /> + <when input="input_format" value="bigwig" format="bigwig" /> + <when input="input_format" value="gff" format="gff" /> + <when input="input_format" value="vcf" format="vcf" /> + <when input="input_format" value="wig" format="bigwig" /> </change_format> </data> <data format="text" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}"> - <filter>multiple.input_format in ["bam" , "vcf"]</filter> + <filter>input_format in ["bam" , "vcf"]</filter> <change_format> - <when input="multiple.input_format" value="bam" format="bam" /> - <when input="multiple.input_format" value="vcf" format="vcf" /> + <when input="input_format" value="bam" format="bam" /> + <when input="input_format" value="vcf" format="vcf" /> </change_format> </data> <data format="text" name="output2" label="${tool.name} (bedgraph) on ${on_string}"> - <filter>multiple.input_format in ["wig"]</filter> + <filter>input_format in ["wig"]</filter> <change_format> - <when input="multiple.input_format" value="wig" format="bedgraph" /> + <when input="input_format" value="wig" format="bedgraph" /> </change_format> </data> </outputs>