Mercurial > repos > brenninc > directory_reader_by_white_black_lists
changeset 1:edd9bc4baf5a draft default tip
Bug fix: fg datatype can also be set to fastq subtype
| author | brenninc |
|---|---|
| date | Wed, 23 Mar 2016 11:11:23 -0400 |
| parents | 6a16b101b35f |
| children | |
| files | data_reader.xml |
| diffstat | 1 files changed, 21 insertions(+), 25 deletions(-) [+] |
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--- a/data_reader.xml Wed Mar 23 10:56:32 2016 -0400 +++ b/data_reader.xml Wed Mar 23 11:11:23 2016 -0400 @@ -61,6 +61,22 @@ --list ${listing} ]]> </command> + <macros> + <xml name="new_galaxy"> + <conditional name="new_galaxy"> + <param name="new_ending" type="select" label="Ending to be used for Galaxy" help="Will determine which down stream tools can be used."> + <option value="fastq" selected="true">Keep data as general fastq format</option> + <option value="fastqsanger">Tag data as fastq sanger in galaxy</option> + <option value="fastqsolexa">Tag data as fastq solexa in galaxy</option> + <option value="fastqillumina">Tag data as fastq illumina in galaxy</option> + </param> + <when value="fastq" /> + <when value="fastqsanger" /> + <when value="fastqsolexa" /> + <when value="fastqillumina" /> + </conditional> + </xml> + </macros> <inputs> <param name="directory" type="text" label="Directory to read data from." /> <param name="list_name" type="text" size="25" label="output name" value="input data"/> @@ -98,34 +114,14 @@ <when value="fasta" /> <when value="fasta.gz" /> <when value="fastq" > - <conditional name="new_galaxy"> - <param name="new_ending" type="select" label="Ending to be used for Galaxy" help="Will determine which down stream tools can be used."> - <option value="fastq" selected="true">Keep data as general fastq format</option> - <option value="fastqsanger">Tag data as fastq sanger in galaxy</option> - <option value="fastqsolexa">Tag data as fastq solexa in galaxy</option> - <option value="fastqillumina">Tag data as fastq illumina in galaxy</option> - </param> - <when value="fastq" /> - <when value="fastqsanger" /> - <when value="fastqsolexa" /> - <when value="fastqillumina" /> - </conditional> + <expand macro="new_galaxy"/> </when> <when value="fastq.gz" > - <conditional name="new_galaxy"> - <param name="new_ending" type="select" label="Ending to be used for Galaxy" help="Will determine which down stream tools can be used."> - <option value="fastq" selected="true" >Keep data as general fastq format</option> - <option value="fastqsanger">Tag data as fastq sanger in galaxy</option> - <option value="fastqsolexa">Tag data as fastq solexa in galaxy</option> - <option value="fastqillumina">Tag data as fastq illumina in galaxy</option> - </param> - <when value="fastq" /> - <when value="fastqsanger" /> - <when value="fastqsolexa" /> - <when value="fastqillumina" /> - </conditional> + <expand macro="new_galaxy"/> </when> - <when value="fq" /> + <when value="fq" > + <expand macro="new_galaxy"/> + </when> <when value="sam" /> <when value="tabular" /> <when value="text" />