comparison scaffold.xml @ 1:0d0cbb69a03f draft

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0:e9981e6af666

  <configfiles>
    <configfile name="sample_config"># Simple format group:group_name followed by pairs of name:name and path:path lines
#if $sample_mode.mode == "full"
#set $samples = $sample_mode.samples
#for $sample in $samples:
#if $sample.category.specify 
#set $category = $sample.category.name
#else
#set $category = $sample.sample_name 
#end if
sample:$sample.sample_name
mudpit:$sample.mudpit
category:$category
#for $sample_input in $sample.sample_inputs:

    --protein_probability '$thresholds.protein_probability' \
    --peptide_probability '$thresholds.peptide_probability' \
    #end if
    #if $advanced.specify
    #if $advanced.output_driver
    --output_driver $output_drirver \
    #end if
    #end if
  </command>
  <inputs>
    <param format="fasta" name="database" type="data" label="Search Database" />

            <when value="false" />
            <when value="true">
              <param name="name" type="text" label="Category Name" help="" />
            </when>
          </conditional>
        </repeat>        
      </when>
      <when value="sample_per_file">
        <param format="t.xml,omx" name="sample_inputs" type="data" multiple="true" label="Input Files" />
      </when>
    </conditional>

      -->
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="xml" name="output_drirver" label="Scaffold Driver for ${on_string}">
      <filter>(advanced['specify'] and advanced["output_driver"])</filter>
    </data>
    <data format="sf3" name="output" />
  </outputs>
  <requirements>

**Citation**

For the underlying tool, please cite `TODO`

If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-scaffold
  </help>
</tool>

1:0d0cbb69a03f

  <configfiles>
    <configfile name="sample_config"># Simple format group:group_name followed by pairs of name:name and path:path lines
#if $sample_mode.mode == "full"
#set $samples = $sample_mode.samples
#for $sample in $samples:
#if $sample.category.specify
#set $category = $sample.category.name
#else
#set $category = $sample.sample_name
#end if
sample:$sample.sample_name
mudpit:$sample.mudpit
category:$category
#for $sample_input in $sample.sample_inputs:

    --protein_probability '$thresholds.protein_probability' \
    --peptide_probability '$thresholds.peptide_probability' \
    #end if
    #if $advanced.specify
    #if $advanced.output_driver
    --output_driver $output_driver \
    #end if
    #end if
  </command>
  <inputs>
    <param format="fasta" name="database" type="data" label="Search Database" />

            <when value="false" />
            <when value="true">
              <param name="name" type="text" label="Category Name" help="" />
            </when>
          </conditional>
        </repeat>
      </when>
      <when value="sample_per_file">
        <param format="t.xml,omx" name="sample_inputs" type="data" multiple="true" label="Input Files" />
      </when>
    </conditional>

      -->
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="xml" name="output_driver" label="Scaffold Driver for ${on_string}">
      <filter>(advanced['specify'] and advanced["output_driver"])</filter>
    </data>
    <data format="sf3" name="output" />
  </outputs>
  <requirements>

**Citation**

For the underlying tool, please cite `TODO`

If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/scaffold
  </help>
</tool>