comparison cuffnorm_wrapper.xml @ 6:28b94cfbfdb9 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm commit 80b06e80066b32ad53ed418628992f056444256f

5:9a854107dbb2

<tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.3">
    <description>Create normalized expression levels</description>
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements" />

        <data format="txt" name="read_groups_info" label="${tool.name} on ${on_string}: Read Groups" from_work_dir="read_groups.info" >
            <filter>(include_read_group_files == 'Yes')</filter>
            <filter>(output_format == 'cuffdiff')</filter>
        </data>
        <!-- simple-table format-->
         <data format="tabular" name="isoforms_attr" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.attr_table" >
            <filter>(include_read_group_files == 'Yes')</filter>
            <filter>(output_format == 'simple-table')</filter>
        </data>
        <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.attr_table" >
            <filter>(include_read_group_files == 'Yes')</filter>
            <filter>(output_format == 'simple-table')</filter>
        </data>
        <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.attr_table" >
            <filter>(include_read_group_files == 'Yes')</filter>
            <filter>(output_format == 'simple-table')</filter>
        </data>
        <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.attr_table" >
            <filter>(include_read_group_files == 'Yes')</filter>
            <filter>(output_format == 'simple-table')</filter>
        </data>

        <!-- Cuffdiff format datasets. -->

6:28b94cfbfdb9

<tool id="cuffnorm" name="Cuffnorm" version="@TOOL_VERSION@.4" profile="@PROFILE@">
    <description>Create normalized expression levels</description>
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements" />

        <data format="txt" name="read_groups_info" label="${tool.name} on ${on_string}: Read Groups" from_work_dir="read_groups.info" >
            <filter>(include_read_group_files == 'Yes')</filter>
            <filter>(output_format == 'cuffdiff')</filter>
        </data>
        <!-- simple-table format-->
        <data format="tabular" name="isoforms_attr" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.attr_table" >
            <filter>(include_read_group_files == 'Yes')</filter>
            <filter>(output_format == 'simple-table')</filter>
        </data>
        <data format="tabular" name="genes_attr" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.attr_table" >
            <filter>(include_read_group_files == 'Yes')</filter>
            <filter>(output_format == 'simple-table')</filter>
        </data>
        <data format="tabular" name="cds_attr" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.attr_table" >
            <filter>(include_read_group_files == 'Yes')</filter>
            <filter>(output_format == 'simple-table')</filter>
        </data>
        <data format="tabular" name="tss_attr" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.attr_table" >
            <filter>(include_read_group_files == 'Yes')</filter>
            <filter>(output_format == 'simple-table')</filter>
        </data>

        <!-- Cuffdiff format datasets. -->