| Previous changeset 7:29a682a7dd16 (2016-06-16) Next changeset 9:1ec00e184217 (2016-06-16) |
|
Commit message:
Uploaded |
|
modified:
vcfs2fasta.xml |
| b |
| diff -r 29a682a7dd16 -r f05fa489089b vcfs2fasta.xml --- a/vcfs2fasta.xml Thu Jun 16 06:40:02 2016 -0400 +++ b/vcfs2fasta.xml Thu Jun 16 06:40:13 2016 -0400 |
| b |
| @@ -17,98 +17,140 @@ </stdio> <command interpreter="bash"> vcfs2fasta.sh - $output - #if str($mix_cond.mix) == "yes": + $output + #if str($mix_cond.mix) == "yes": $mix_cond.mix_value #else NOTTHERE #end if - #if str($cols_cond.cols) == "yes": - $cols_cond.column_ns + #if str($coln_cond.coln) == "yes": + $coln_cond.column_ns #else NOTTHERE #end if - #if str($sample_cond.sample) == "yes": - $sample_cond.sample_ns + #if str($colgap_cond.colgap) == "yes": + $colgap_cond.column_ns + #else + NOTTHERE + #end if + #if str($samplen_cond.samplen) == "yes": + $samplen_cond.sample_ns + #else + NOTTHERE + #end if + #if str($samplegap_cond.samplegap) == "yes": + $samplegap_cond.sample_gaps #else NOTTHERE #end if - #if str($reference_cond.reference) == "yes": - $reference_cond.ref_fa - #else + #if str($reference_cond.reference) == "yes": + $reference_cond.ref_fa + #else + NOTTHERE + #end if + #if str($include_cond.include) == "yes": + $include_cond.in_bed + #else NOTTHERE #end if - #if str($include_cond.include) == "yes": - $include_cond.in_bed - #else + #if str($exclude_cond.exclude) == "yes": + $exclude_cond.ex_bed + #else NOTTHERE #end if - #if str($exclude_cond.exclude) == "yes": - $exclude_cond.ex_bed - #else + #if $withstats: + $statsfile + #else NOTTHERE #end if - #for $i, $input_vcf in enumerate( $input_vcfs ): + #for $i, $input_vcf in enumerate( $input_vcfs ): "${input_vcf}" #end for </command> <inputs> - <param name="input_vcfs" type="data" multiple="true" format="vcf" label="Input VCF file(s)" /> - <conditional name="mix_cond"> + <param name="input_vcfs" type="data" multiple="true" format="vcf" label="Input VCF file(s)" /> + + <conditional name="mix_cond"> <param name="mix" type="select" label="With Mixtures" help="Specify this option with a threshold to output mixtures above this threshold."> <option value="yes">Specify</option> <option value="no" selected="true">Do not specify</option> </param> <when value="yes"> - <param name="mix_value" type="float" value="0.5" label="Mixture value" /> + <param name="mix_value" type="float" value="0.5" label="Mixture value" /> </when> </conditional> - <conditional name="cols_cond"> - <param name="cols" type="select" label="Column Ns" help="Keeps columns with fraction of Ns below specified threshold."> + + <conditional name="coln_cond"> + <param name="coln" type="select" label="Column Ns" help="Keeps columns with fraction of Ns below specified threshold."> + <option value="yes">Specify</option> + <option value="no" selected="true">Do not specify</option> + </param> + <when value="yes"> + <param name="column_ns" type="float" value="0.5" label="Column Ns value" /> + </when> + </conditional> + + <conditional name="colgap_cond"> + <param name="colgap" type="select" label="Column Gaps" help="Keeps columns with fraction of gaps below specified threshold."> <option value="yes">Specify</option> <option value="no" selected="true">Do not specify</option> </param> <when value="yes"> - <param name="column_ns" type="float" value="0.5" label="Column Ns value" /> + <param name="column_gaps" type="float" value="0.5" label="Column gaps value" /> </when> </conditional> - <conditional name="sample_cond"> - <param name="sample" type="select" label="Sample Ns" help="Keeps samples with fraction of Ns below specified threshold."> + + <conditional name="samplen_cond"> + <param name="samplen" type="select" label="Sample Ns" help="Keeps samples with fraction of Ns below specified threshold."> <option value="yes">Specify</option> <option value="no" selected="true">Do not specify</option> </param> <when value="yes"> - <param name="sample_ns" type="float" value="0.5" label="Sample Ns value" /> + <param name="sample_ns" type="float" value="0.5" label="Sample Ns value" /> </when> </conditional> - <conditional name="reference_cond"> + + <conditional name="samplegap_cond"> + <param name="samplegap" type="select" label="Sample gaps" help="Keeps samples with fraction of gaps below specified threshold."> + <option value="yes">Specify</option> + <option value="no" selected="true">Do not specify</option> + </param> + <when value="yes"> + <param name="sample_gaps" type="float" value="0.5" label="Sample gaps value" /> + </when> + </conditional> + + <conditional name="reference_cond"> <param name="reference" type="select" label="Reference genome file" help="If path to reference specified, then whole genome will be outputted."> <option value="yes">Specify</option> <option value="no" selected="true">Do not specify</option> </param> <when value="yes"> - <param name="ref_fa" type="data" format="fasta" label="Reference fasta file" help="Fasta format"/> + <param name="ref_fa" type="data" format="fasta" label="Reference fasta file" help="Fasta format"/> </when> </conditional> - <conditional name="include_cond"> + + <conditional name="include_cond"> <param name="include" type="select" label="Include region" help="Specify regions to include in a bed file."> <option value="yes">Specify</option> <option value="no" selected="true">Do not specify</option> </param> <when value="yes"> - <param name="in_bed" type="data" format="bed" label="Include regions bed file" help="bed format"/> + <param name="in_bed" type="data" format="bed" label="Include regions bed file" help="bed format"/> </when> </conditional> - <conditional name="exclude_cond"> + + <conditional name="exclude_cond"> <param name="exclude" type="select" label="Exclude region" help="Specify regions to exclude in a bed file."> <option value="yes">Specify</option> <option value="no" selected="true">Do not specify</option> </param> <when value="yes"> - <param name="ex_bed" type="data" format="bed" label="Exclude regions bed file" help="bed format"/> + <param name="ex_bed" type="data" format="bed" label="Exclude regions bed file" help="bed format"/> </when> </conditional> + </inputs> <outputs> |