comparison igvtools_tile.xml @ 1:ae2bc4e5fefc draft default tip

Fix igvtools_tile.xml tdf output and add log file output

0:2eb1e2924c1a

<tool id="igvtools_tile" name="IGVtools tile" version="1.0">
  <description>convert a sorted data input file to a binary tiled data (.tdf) file</description>
  <command interpreter="bash">igvtools tile 
    #if $zoom.__str__ != '':
      -z $zoom
    #end if

    #elif $input.datatype.file_ext == 'igv.cn':
       #set $input_name='input_file.cn'
    #elif $input.datatype.file_ext == 'igv':
       #set $input_name='input_file.igv'
    #end if
    `ln -s $input  $input_name; echo $input_name` $output_tdf $refGenomeSource.ref
  </command>
  <inputs>
    <conditional name="refGenomeSource">
      <param name="refGenomeSource_type" type="select" label="Will you select a reference genome from your history or use a built-in reference?">
        <option value="built-in">Use a built-in reference</option>

                   chr start end name
                 where name is the probe name in the .gct file."/>
  </inputs>
  <outputs>
    <data format="igv.tdf" name="output_tdf" metadata_source="input" label="${tool.name} on ${on_string}: igv.tdf" from_work_dir="output.tdf"/>
  </outputs>
  <tests>
  </tests>
  <help>
**What it does**

1:ae2bc4e5fefc

<tool id="igvtools_tile" name="IGVtools tile" version="1.1">
  <description>convert a sorted data input file to a binary tiled data (.tdf) file</description>
  <command interpreter="bash">igvtools tile 
    #if $zoom.__str__ != '':
      -z $zoom
    #end if

    #elif $input.datatype.file_ext == 'igv.cn':
       #set $input_name='input_file.cn'
    #elif $input.datatype.file_ext == 'igv':
       #set $input_name='input_file.igv'
    #end if
    `ln -s $input  $input_name; echo $input_name` output.tdf $refGenomeSource.ref 1> igv.stdout
  </command>
  <inputs>
    <conditional name="refGenomeSource">
      <param name="refGenomeSource_type" type="select" label="Will you select a reference genome from your history or use a built-in reference?">
        <option value="built-in">Use a built-in reference</option>

                   chr start end name
                 where name is the probe name in the .gct file."/>
  </inputs>
  <outputs>
    <data format="igv.tdf" name="output_tdf" metadata_source="input" label="${tool.name} on ${on_string}: igv.tdf" from_work_dir="output.tdf"/>
    <data format="txt" name="logfile" metadata_source="input" label="${tool.name} on ${on_string}: igv.log" from_work_dir="igv.stdout"/>
  </outputs>
  <tests>
  </tests>
  <help>
**What it does**