annotate cravatp_submit.xml @ 3:a018c44dc18b draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatp_score_and_annotate commit d80e60ce74aabe64e131d560085af099d52b81cf-dirty

<tool id="cravatp_submit" name="CRAVAT-P Submit, Intersect, Check, and Retrieve" version="1.1.0">
    <description>| Submits, intersects, checks for, and retrieves data for cancer annotation.</description>
  <command detect_errors="aggressive">
  <![CDATA[
#if $proteo.proteoInput == 'yes':
    #if '$analysis.type' == 'CHASM' or '$analysis.type' == 'CHASM+VEST':
        python '$__tool_directory__/cravatp_submit.py' '$input' '$GRCh' '$variant' '$gene' '$noncoding' '$error' '$analysis.type' --classifier '$analysis.classifier' --proBED '$proBED' Do-allIntersect '$proteo.intersectedVariants' --vcfOutput '$vcf_output'
    #else: 
        python '$__tool_directory__/cravatp_submit.py' '$input' '$GRCh' '$variant' '$gene' '$noncoding' '$error' '$analysis.type' --proBED '$proBED' --allIntersect '$proteo.intersectedVariants' --vcfOutput '$vcf_output' 
    #end if
#else:
    #if $analysis.type == 'CHASM' or $analysis.type == 'CHASM+VEST':
        python '$__tool_directory__/cravatp_submit.py' '$input' '$GRCh' '$variant' '$gene' '$noncoding' '$error' '$analysis.type' --classifier '$analysis.classifier' 
    #else: 
        python '$__tool_directory__/cravatp_submit.py' '$input' '$GRCh' '$variant' '$gene' '$noncoding' '$error' '$analysis.type'
    #end if
#end if
]]></command>
  
  <inputs>
    <param format="vcf" name="input" type="data" label="Source file" help="Accepts transcriptomic or genomic inputs (e.g., tabular, VCF). Additional details can be found below."></param>
    <conditional name="proteo">
      <param name="proteoInput" type="select" label="Intersect with proteogenomic input?" help="Source file (first input) must be in genomic input to enable intersection with this proteogenomic file. Only variants intersected between the genomic and proteogenomic files are annotated, unless specified otherwise below.">
        <option value="yes">Yes</option>
        <option value="no" selected="true">No</option>
      </param>
      <when value="yes">
        <param format="BED" name="proBED" type="data" label="Peptides with Genomic Coordinates (ProBED Format)"></param>
        <param name="intersectedVariants" type="boolean" checked="false" label="Submit all variants?" help="Submits all variants, including non-intersected variants, to the CRAVAT server. This results in a complete genomic analysis at the expense of a longer runtime."></param>
        <param name="output_vcf" type="boolean" checked="false" label="Output intersected genomic file?" help="The intersected genomic file (e.g., VCF) will be included as a result."></param>
      </when>
      <when value="no">
      </when>
    </conditional>
    <conditional name="analysis">
      <param format="tabular" name="type" type="select" label="Analysis Program" help="CHASM and VEST are machine learning methods for predicting the functional significance and pathogenicity of variants, respectively.">
          <option value="None">None</option>
          <option value="CHASM">CHASM</option>
          <option value="VEST">VEST</option>
          <option value="CHASM+VEST">CHASM and VEST</option>
      </param>
      <when value="None"/>
      <when value="VEST"/>
      <when value="CHASM">
        <param format="tabular" name="classifier" type="select" label="CHASM Classifier">
          <option value="Bladder">Bladder</option>
          <option value="Blood-Lymphocyte">Blood-Lymphocyte</option>
          <option value="Blood-Myeloid">Blood-Myeloid</option>
          <option value="Brain-Glioblastoma-Multiforme">Brain-Glioblastoma-Multiforme</option>
          <option value="Brain-Lower-Grade-Glioma">Brain-Lower-Grade-Glioma</option>
          <option value="Breast">Breast</option>
          <option value="Cervix">Cervix</option>
          <option value="Colon">Colon</option>
          <option value="GID">GID</option>
          <option value="Head-and-Neck">Head-and-Neck</option>
          <option value="Kidney-Chromophobe">Kidney-Chromophobe</option>
          <option value="Kidney-Clear-Cell">Kidney-Clear-Cell</option>
          <option value="Kidney-Papillary-Cell">Kidney-Papillary-Cell</option>
          <option value="Liver-Nonviral">Liver-Nonviral</option>
          <option value="Liver-Viral">Liver-Viral</option>
          <option value="Lung-Adenocarcinoma">Lung-Adenocarcinoma</option>
          <option value="Lung-Squamous-Cell">Lung-Squamous-Cell</option>
          <option value="Other">Other</option>
          <option value="Ovary">Ovary</option>
          <option value="Pancreas">Pancreas</option>
          <option value="Prostate-Adenocarcinoma">Prostate-Adenocarcinoma</option>
          <option value="Rectum">Rectum</option>
          <option value="Skin">Skin</option>
          <option value="Stomach">Stomach</option>
          <option value="Thyroid">Thyroid</option>
          <option value="Uterus">Uterus</option>
        </param>
      </when>
      <when value="CHASM+VEST">
        <param format="tabular" name="classifier" type="select" label="CHASM Classifier">
          <option value="Bladder">Bladder</option>
          <option value="Blood-Lymphocyte">Blood-Lymphocyte</option>
          <option value="Blood-Myeloid">Blood-Myeloid</option>
          <option value="Brain-Glioblastoma-Multiforme">Brain-Glioblastoma-Multiforme</option>
          <option value="Brain-Lower-Grade-Glioma">Brain-Lower-Grade-Glioma</option>
          <option value="Breast">Breast</option>
          <option value="Cervix">Cervix</option>
          <option value="Colon">Colon</option>
          <option value="GID">GID</option>
          <option value="Head-and-Neck">Head-and-Neck</option>
          <option value="Kidney-Chromophobe">Kidney-Chromophobe</option>
          <option value="Kidney-Clear-Cell">Kidney-Clear-Cell</option>
          <option value="Kidney-Papillary-Cell">Kidney-Papillary-Cell</option>
          <option value="Liver-Nonviral">Liver-Nonviral</option>
          <option value="Liver-Viral">Liver-Viral</option>
          <option value="Lung-Adenocarcinoma">Lung-Adenocarcinoma</option>
          <option value="Lung-Squamous-Cell">Lung-Squamous-Cell</option>
          <option value="Other">Other</option>
          <option value="Ovary">Ovary</option>
          <option value="Pancreas">Pancreas</option>
          <option value="Prostate-Adenocarcinoma">Prostate-Adenocarcinoma</option>
          <option value="Rectum">Rectum</option>
          <option value="Skin">Skin</option>
          <option value="Stomach">Stomach</option>
          <option value="Thyroid">Thyroid</option>
          <option value="Uterus">Uterus</option>
        </param>
      </when>
    </conditional>
    <!-- TODO: programatically retrieve the GRCh from a dataset rather than manually selecting it.-->
    <param format="tabular" name="GRCh" type="select" label="Genome Reference Consortium Human Build (GRCh)" 
        help="The default human reference genome used for annotation is GRCh38, released on December 24th, 2013 from the Genome Reference Consortium.">
      <option value="GRCh38">GRCh38/hg38</option>
      <option value="GRCh37">GRCh37/hg19</option>
    </param>
  </inputs>
  <outputs>
    <collection name="results" type="list" label="CRAVAT-P Results on ${on_string}">
      <data format="tabular" label="CRAVAT: gene Level Annotation Report on ${on_string}" name="gene" />
      <data format="tabular" label="CRAVAT: Variant Report on ${on_string}" name="variant" />
      <data format="tabular" label="CRAVAT: Non-coding Variant Report on ${on_string}" name="noncoding" />
      <data format="tabular" label="CRAVAT: Errors on ${on_string}" name="error" />
    </collection>
    <data format="vcf" label="Intersected VCF on ${on_string}" name="vcf_output">
        <filter>proteo['proteoInput'] == 'yes' and proteo['output_vcf']</filter>
      </data>
  </outputs>
  <tests>
    <!-- Proteogenomic test case -->
    <test>
      <param name="input" value="Freebayes_one-variant.vcf"/>
      <param name="GRCh" value="GRCh38"/>
      <param name="variant" value="variant.tsv"/>
      <param name="gene" value="gene.tsv"/>
      <param name="noncoding" value="noncoding.tsv"/>
      <param name="error" value="error.tsv"/>
      <param name="type" value="CHASM" />
      <param name="classifier" value="Breast" />
      <param name="proteoInput" value="yes" />
      <param name="proBED" value="MCF7_proBed.bed"/>
      <output_collection name="results" type="list">
        <element name="variant">
          <assert_contents>
            <has_text text="hg38"/>
            <has_text text="UPF1" />
            <not_has_text text="CRABP2"/>
          </assert_contents>
        </element>
      </output_collection>
    </test>
    <!-- GRCh38/hg38 and no analysis test case -->
    <test>
      <param name="input" value="Freebayes_one-variant.vcf"/>
      <param name="GRCh" value="GRCh38"/>
      <param name="variant" value="variant.tsv"/>
      <param name="gene" value="gene.tsv"/>
      <param name="noncoding" value="noncoding.tsv"/>
      <param name="error" value="error.tsv"/>
      <param name="type" value="None"/>
      <output_collection name="results" type="list">
        <element name="variant">
          <assert_contents>
            <has_text text="#Variant Report" />
            <has_text text="hg38"/>
            <has_text text="UPF1" />
            <not_has_text text="VEST" />
          </assert_contents>
        </element>
      </output_collection>
    </test>
     <!-- GRCh38/hg38 and no analysis test case -->
    <test>
      <param name="input" value="Freebayes_one-variant.vcf"/>
      <param name="GRCh" value="GRCh38"/>
      <param name="variant" value="variant.tsv"/>
      <param name="gene" value="gene.tsv"/>
      <param name="noncoding" value="noncoding.tsv"/>
      <param name="error" value="error.tsv"/>
      <param name="type" value="None"/>
      <output_collection name="results" type="list">
        <element name="variant">
          <assert_contents>
            <has_text text="#Variant Report" />
            <has_text text="hg38"/>
            <has_text text="UPF1" />
            <not_has_text text="VEST" />
          </assert_contents>
        </element>
      </output_collection>
    </test>
    <!-- GRCh37/hg19 and no analysis test case -->
    <test>
      <param name="input" value="Freebayes_one-variant.vcf"/>
      <param name="GRCh" value="GRCh37"/>
      <param name="variant" value="variant.tsv"/>
      <param name="gene" value="gene.tsv"/>
      <param name="noncoding" value="noncoding.tsv"/>
      <param name="error" value="error.tsv"/>
      <param name="type" value="None"/>
      <output_collection name="results" type="list">
        <element name="variant">
          <assert_contents>
            <has_text text="#Variant Report" />
            <has_text text="hg19"/>
            <not_has_text text="VEST" />
          </assert_contents>
        </element>
      </output_collection>
    </test>
    <!-- CHASM with "Breast" classifier test case -->
    <test>
      <param name="input" value="Freebayes_one-variant.vcf"/>
      <param name="GRCh" value="GRCh38"/>
      <param name="variant" value="variant.tsv"/>
      <param name="gene" value="gene.tsv"/>
      <param name="noncoding" value="noncoding.tsv"/>
      <param name="error" value="error.tsv"/>
      <param name="type" value="CHASM"/>
      <param name="classifier" value="Breast"/>
      <output_collection name="results" type="list">
        <element name="variant">
          <assert_contents>
            <has_text text="hg38"/>
            <has_text text="UPF1" />
            <has_text text="Breast" />
            <has_text text="#Variant Report" />
            <not_has_text text="VEST" />
          </assert_contents>
        </element>
      </output_collection>
    </test>
    
    <!-- "Output intersected VCF" test case -->
    <test>
      <param name="input" value="Freebayes_one-variant.vcf"/>
      <param name="GRCh" value="GRCh38"/>
      <param name="variant" value="variant.tsv"/>
      <param name="gene" value="gene.tsv"/>
      <param name="noncoding" value="noncoding.tsv"/>
      <param name="error" value="error.tsv"/>
      <param name="type" value="CHASM" />
      <param name="classifier" value="Breast" />
      <param name="proteoInput" value="yes" />
      <param name="proBED" value="MCF7_proBed.bed"/>
      <param name="output_vcf" value="true"/>
      <output name="vcf_output" file="results/intersected_vcf.vcf"/>
    </test>
    <!-- "All proteogenomic variants submitted" test case-->
    <test>
      <param name="input" value="Freebayes_two-variants.vcf"/>
      <param name="GRCh" value="GRCh38"/>
      <param name="variant" value="variant.tsv"/>
      <param name="gene" value="gene.tsv"/>
      <param name="noncoding" value="noncoding.tsv"/>
      <param name="error" value="error.tsv"/>
      <param name="type" value="CHASM" />
      <param name="classifier" value="Breast" />
      <param name="proteoInput" value="yes" />
      <param name="proBED" value="MCF7_proBed.bed"/>
      <param name="intersectedVariants" value="true" />
      <output_collection name="results" type="list">
        <element name="variant">
          <assert_contents>
            <has_text text="hg38"/>
            <has_text text="UPF1" />
            <has_text text="CRABP2"/>
          </assert_contents>
        </element>
      </output_collection>
    </test>
    <!-- "Only intersected proteogenomic variants submitted" test case-->
    <test>
      <param name="input" value="Freebayes_two-variants.vcf"/>
      <param name="GRCh" value="GRCh38"/>
      <param name="variant" value="variant.tsv"/>
      <param name="gene" value="gene.tsv"/>
      <param name="noncoding" value="noncoding.tsv"/>
      <param name="error" value="error.tsv"/>
      <param name="type" value="CHASM" />
      <param name="classifier" value="Breast" />
      <param name="proteoInput" value="yes" />
      <param name="proBED" value="MCF7_proBed.bed"/>
      <param name="intersectedVariants" value="true" />
      <output_collection name="results" type="list">
        <element name="variant">
          <assert_contents>
            <has_text text="#Variant Report" />
            <has_text text="hg38"/>
            <has_text text="UPF1" />
            <has_text text="EAIDSPVSFLVLHNQIR" />
          </assert_contents>
        </element>
      </output_collection>
    </test>
  </tests>
  <help><![CDATA[
    This tool submits, checks for, and retrieves data for cancer annotation from the CRAVAT platform at https://www.cravat.us. 
    For additional details on input format, visit this link: http://cravat.us/CRAVAT/help.jsp.

-----

**Input Type Example:**

  CRAVAT Format (*Genomic-coordinate format*)

    =====  =====  =========  ======  =========  =========  ====================
    UID    Chr.   Position   Strand  Ref. base  Alt. base  Sample ID (optional)
    =====  =====  =========  ======  =========  =========  ====================
    TR1    chr17  7674188    \-      G          T          TCGA-02-0231
    TR2    chr10  121520166  \-      G          A          TCGA-02-3512
    TR3    chr13  48459831   \+      C          A          TCGA-02-3532
    TR4    chr7   116777451  \+      G          T          TCGA-02-1523
    TR5    chr7   140753336  \-      T          A          TCGA-02-0023
    TR6    chr17  39724745   \+      G          T          TCGA-02-0252
    Ins1   chr17  39724745   \+      \-         T          TCGA-02-0252
    Del1   chr17  39724745   \+      A          \-         TCGA-02-0252
    CSub1  chr2   39644095   \+      ATGCT      GA         TCGA-02-0252
    =====  =====  =========  ======  =========  =========  ====================
]]>
  </help>
  <citations>
    <citation type="doi">10.1021/acs.jproteome.8b00404</citation>
    <citation type="doi">10.1158/0008-5472.CAN-17-0338</citation>
    <citation type="doi">10.1186/s13059-017-1377-x</citation>
  </citations>
</tool>