Mercurial > repos > galaxyp > cravatool
diff cravatp_submit.xml @ 1:2c7bcc1219fc draft
Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
| author | galaxyp |
|---|---|
| date | Thu, 16 Aug 2018 12:27:35 -0400 |
| parents | |
| children | a018c44dc18b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravatp_submit.xml Thu Aug 16 12:27:35 2018 -0400 @@ -0,0 +1,296 @@ +<tool id="cravatp_submit" name="CRAVAT-P Submit, Intersect, Check, and Retrieve" version="1.0.0"> + <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 '$proBED' --intersectOnly '$proteo.intersectedVariants' --vcfOutput '$vcf_output' + #else: + python '$__tool_directory__/cravatp_submit.py' '$input' '$GRCh' '$variant' '$gene' '$noncoding' '$error' '$analysis.type' --proBED '$proBED' --intersectOnly '$proteo.intersectedVariants' --vcfOutput '$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."> + <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 only intersected variants?" help="Submits the intersected portion of the genomic file to CRAVAT's server. Restricting analysis to only intersected variants takes less time but also provides less-comprehensive results."></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="VEST and CHASM are machine learning methods for predicting the pathogenicity and functional significance 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 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> + <!-- 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> + <!-- 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="#Variant Report" /> + <has_text text="hg38"/> + <has_text text="UPF1" /> + <has_text text="EAIDSPVSFLVLHNQIR" /> + </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> + <!-- "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="hg38"/> + <has_text text="UPF1" /> + <not_has_text text="CRABP2"/> + </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">10.1158/0008-5472.CAN-17-0338</citation> + <citation type="doi">10.1186/s13059-017-1377-x</citation> + </citations> +</tool>