<tool id="tcga_import" name="TCGA Import" version="1.0.0">
  <description>TCGA Import</description>
  <command interpreter="python">tcgaImport.py 
-w ./
#if $iparam.import_mode == "uuid":
--uuid-download ${out_uuid}
#end if
#if $iparam.import_mode == "sample_list":
--samples > ${out_sample_list}
#end if
#if $iparam.import_mode == "archive_list":
-z > ${archive_list_out}
#end if
#if $iparam.import_mode == "archive":
-m ${__tool_data_path__}
--download -
--basename ${iparam.base}
#if str($iparam.uuid_mapping) != "None":
--uuid ${iparam.uuid_mapping}
#end if
--out ${archive_out}
--out-meta ${archive_meta}
#end if
#if $iparam.import_mode == "clinical_list":
--all-clinical > ${clinical_list_out}
#end if
#if $iparam.import_mode == "clinical":
-m ${__tool_data_path__}
--download -
--clinical-basename ${iparam.clinical_archive}
--out-clinical patient ${out_patient} ${out_patient_meta}
--out-clinical sample ${out_sample} ${out_sample_meta}
--out-clinical radiation ${out_radiation} ${out_radiation_meta}
--out-clinical drug ${out_drug} ${out_drug_meta}
--out-clinical portion ${out_portion} ${out_portion_meta}
--out-clinical analyte ${out_analyte} ${out_analyte_meta}
--out-clinical aliquot ${out_aliquot} ${out_aliquot_meta}

#end if
  </command>
  <inputs>
      <conditional name="iparam">
        <param name="import_mode" type="select" label="Import Mode">
          <option value="uuid">TCGA UUID/Barcode Mapping</option>
          <option value="sample_list">TCGA Sample List</option>
          <option value="archive_list">List TCGA Archives</option>
          <option value="archive">Import Archive</option>
          <option value="clinical_list">List TCGA Clinical Data</option>
          <option value="clinical">Clinical Import</option>
        </param>
        <when value="uuid"/>
        <when value="samples"/>
        <when value="archive_list"/>
        <when value="archive">
          <param name="base" type="text" size="90" value="unc.edu_COAD_IlluminaHiSeq_RNASeqV2" label="Archive Basename"/>
          <param name="uuid_mapping" type="data" format="tabular" optional="true" label="UUID-Barcode Mapping"/>
        </when>
        <when value="clinical_list"/>
        <when value="clinical">
          <param name="clinical_archive" size="90" value="intgen.org_OV_bio" type="text"/>          
        </when>
      </conditional>
  </inputs>
  <outputs>
    <data name="out_uuid" format="tabular" label="UUID/Barcode Mapping">
      <filter>iparam['import_mode'] == "uuid"</filter>
    </data>
    <data name="out_sample_list" format="tabular" label="TCGA Samples">
      <filter>iparam['import_mode'] == "sample_list"</filter>
    </data>
    <data name="archive_list_out" format="tabular" label="TCGA Archive List">
      <filter>iparam['import_mode'] == "archive_list"</filter>
    </data>
    <data name="archive_out" format="tabular" label="${iparam.base}">
      <filter>iparam['import_mode'] == "archive"</filter>
    </data>
    <data name="archive_meta" format="txt" label="${iparam.base} Meta">
      <filter>iparam['import_mode'] == "archive"</filter>
    </data>

    <data name="clinical_list_out" format="tabular" label="TCGA Clinical List">
      <filter>iparam['import_mode'] == "clinical_list"</filter>
    </data>


    <data name="out_patient" format="tabular" label="${iparam.clinical_archive} Patient">
        <filter>iparam['import_mode'] == "clinical"</filter>
    </data>
    <data name="out_sample" format="tabular" label="${iparam.clinical_archive} Sample">
        <filter>iparam['import_mode'] == "clinical"</filter>
    </data>
    <data name="out_radiation" format="tabular" label="${iparam.clinical_archive} Radiation">
        <filter>iparam['import_mode'] == "clinical"</filter>
    </data>
    <data name="out_drug" format="tabular" label="${iparam.clinical_archive} Drug">
        <filter>iparam['import_mode'] == "clinical"</filter>
    </data>
    <data name="out_portion" format="tabular" label="${iparam.clinical_archive} Portion">
        <filter>iparam['import_mode'] == "clinical"</filter>
    </data>
    <data name="out_analyte" format="tabular" label="${iparam.clinical_archive} Analyte">
        <filter>iparam['import_mode'] == "clinical"</filter>
    </data>
    <data name="out_aliquot" format="tabular" label="${iparam.clinical_archive} Aliquot">
        <filter>iparam['import_mode'] == "clinical"</filter>
    </data> 

    <data name="out_patient_meta" format="txt" label="${iparam.clinical_archive} Patient Meta">
        <filter>iparam['import_mode'] == "clinical"</filter>
    </data>
    <data name="out_sample_meta" format="txt" label="${iparam.clinical_archive} Sample Meta">
        <filter>iparam['import_mode'] == "clinical"</filter>
    </data>
    <data name="out_radiation_meta" format="txt" label="${iparam.clinical_archive} Radiation Meta">
        <filter>iparam['import_mode'] == "clinical"</filter>
    </data>
    <data name="out_drug_meta" format="txt" label="${iparam.clinical_archive} Drug Meta">
        <filter>iparam['import_mode'] == "clinical"</filter>
    </data>
    <data name="out_portion_meta" format="txt" label="${iparam.clinical_archive} Portion Meta">
        <filter>iparam['import_mode'] == "clinical"</filter>
    </data>
    <data name="out_analyte_meta" format="txt" label="${iparam.clinical_archive} Analyte Meta">
        <filter>iparam['import_mode'] == "clinical"</filter>
    </data>
    <data name="out_aliquot_meta" format="txt" label="${iparam.clinical_archive} Aliquot Meta">
        <filter>iparam['import_mode'] == "clinical"</filter>
    </data> 


  </outputs>
  <help>
TCGA Import Tool
================

An import tool for data from `The Cancer Genome Atlas Data &lt;https://tcga-data.nci.nih.gov&gt;`_.
This tool specializes in importing Level 3, publically accessable data from the TCGA. This includes
processed genomic data and a majority of the clinical info. While this data is publically avalible, it 
is frequently in a varity of file formats that need to be colated and formated before anlyitcal use. This tool
attempts to read across a family of tarballs and compile the data into a single matrix. 
There are also import mechanism to find TCGA sample id lists and UUID conversion tables.

Modes:

*TCGA UUID/Barcode Mapping*
  A two column mapping from TCGA UUID to barcode IDs

*TCGA Sample List*
   A list of TCGA samples, with sample type, cancer type, and platform.

*List TCGA Archives*
   A list of all valid archives found at TCGA.

*Import Archive*
   Import a TCGA archive using a name found in the archive list. This will store a mirror 
   of downloaded files in the Galaxy tool-data folder. This will either produce a matrix or
   BED5 file, with an associated meta data description in JSON
      
*List TCGA Clinical Data*
   List all valid TCGA clinical repositories

*Clinical Import*
   Import a TCGA clinical repository using a name found in the clinical data list. This will store
   a mirror of downloaded files in the Galaxt tool-data folder. This produces 7 matrices and their 
   associated meta data. The different levels of clinical matrix include

    - patient
    - sample
    - radiation
    - drug
    - portion
    - analyte
    - aliquot   


Note: TCGA archive can be large, and this isn't the most optimized piece of code in the world, so import can take a while for some 
of the larger TCGA archives.


  </help>
</tool>