comparison cuffnorm_wrapper.xml @ 1:14a78720e7de draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

0:faa22754dac5

<tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.0">
    <description>Create normalized expression levels</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
      <import>cuff_macros.xml</import>

        </data>
        <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" >
            <filter>(include_read_group_files == 'Yes')</filter>
            <filter>(output_format == 'cuffdiff')</filter>
        </data>
        <data format="text" name="read_groups_info" label="${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" >

    <help>
**Cuffnorm Overview**

Cuffnorm is part of Cufflinks_. Running Cuffnorm is very similar to running Cuffdiff. Cuffnorm takes a GTF2/GFF3 file of transcripts as input, along with two or more SAM, BAM, or CXB files for two or more samples. It produces a number of output files that contain expression levels and normalized fragment counts at the level of transcripts, primary transcripts, and genes. It also tracks changes in the relative abundance of transcripts sharing a common transcription start site, and in the relative abundances of the primary transcripts of each gene. Tracking the former allows one to see changes in splicing, and the latter lets one see changes in relative promoter use within a gene.. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621

.. _Cufflinks: http://cufflinks.cbcb.umd.edu/
        
------

**Know what you are doing**

.. class:: warningmark

There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.

.. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff

------

**Input format**

1:14a78720e7de

<tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.1">
    <description>Create normalized expression levels</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
      <import>cuff_macros.xml</import>

        </data>
        <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" >
            <filter>(include_read_group_files == 'Yes')</filter>
            <filter>(output_format == 'cuffdiff')</filter>
        </data>
        <data format="txt" name="read_groups_info" label="${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" >

    <help>
**Cuffnorm Overview**

Cuffnorm is part of Cufflinks_. Running Cuffnorm is very similar to running Cuffdiff. Cuffnorm takes a GTF2/GFF3 file of transcripts as input, along with two or more SAM, BAM, or CXB files for two or more samples. It produces a number of output files that contain expression levels and normalized fragment counts at the level of transcripts, primary transcripts, and genes. It also tracks changes in the relative abundance of transcripts sharing a common transcription start site, and in the relative abundances of the primary transcripts of each gene. Tracking the former allows one to see changes in splicing, and the latter lets one see changes in relative promoter use within a gene.. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621

.. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/

------

**Know what you are doing**

.. class:: warningmark

There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.

.. __: http://cole-trapnell-lab.github.io/cufflinks/cuffnorm/

------

**Input format**