Mercurial > repos > jbrayet > sequenza

--- a/sequenza_wrapper.xml	Fri Aug 21 05:46:18 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,166 +0,0 @@
-<!--Sequenza - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>
-Copyright (C) 2015  Institut Curie
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.-->
-<tool id="sequenza_tool" name="Sequenza" version="1.2">
-  <description>allele-specific copy number and mutation profiles</description>
-  <requirements>
-    <requirement type="package" version="2.11.1">fontconfig</requirement>
-    <requirement type="package" version="2.7">python</requirement>
-    <requirement type="package" version="2.1.1">sequenza</requirement>
-    <requirement type="package" version="1.2">samtools</requirement>
-  </requirements>
-  <command interpreter="python">
-    sequenza_wrapper.py -name $sampleName -outGalaxy $HTMLFile -format $fileFormat.format -estimation $usePersonalEstimation.estimation -gcContent $gc_content_file
-    #if $fileFormat.format == "BAM":
-      #if $fileFormat.reference_source.reference_source_selector=="cached":
-        -normal $fileFormat.reference_source.normal_file
-        -tumor $fileFormat.reference_source.tumor_file
-        -ref_file $fileFormat.reference_source.ref_file.fields.path
-	-samtools_options '
-	$fileFormat.skip_anomalous_read_pairs
-        $fileFormat.disable_probabilistic_realignment
-	-d "$fileFormat.max_reads_per_bam"
-        -q "$fileFormat.minimum_mapping_quality"
-        -Q "$fileFormat.minimum_base_quality"
-	'
-      #else:
-        -normal $fileFormat.reference_source.normal_file
-        -tumor $fileFormat.reference_source.tumor_file
-        -ref_file $fileFormat.reference_source.ref_file
-	-samtools_options '
-	$fileFormat.skip_anomalous_read_pairs
-        $fileFormat.disable_probabilistic_realignment
-	-d "$fileFormat.max_reads_per_bam"
-        -q "$fileFormat.minimum_mapping_quality"
-        -Q "$fileFormat.minimum_base_quality"
-	'
-      #end if
-    #else:
-      -normal $fileFormat.normal_file
-      -tumor $fileFormat.tumor_file
-    #end if
-    #if $usePersonalEstimation.estimation == "yes":
-      -cellularity $usePersonalEstimation.cellularity
-      -ploidy $usePersonalEstimation.ploidy
-    #end if
-  </command>
-  <inputs>
-    <param name="sampleName" type="text" value="sample" size="30" label="Sample name">
-      <sanitizer invalid_char="">
-        <valid initial="string.letters,string.digits"><add value="_"/></valid>
-      </sanitizer>
-    </param>
-    <conditional name="fileFormat">
-      <param name="format" type="select" label="File format" >
-        <option value="BAM" selected="true">BAM</option>
-        <option value="pileup" >Pileup</option>
-        <option value="pileup_gz" >Pileup.gz</option>
-      </param>
-      <when value="BAM">
-        <conditional name="reference_source">
-      	  <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-            <option value="cached">Locally cached</option>
-            <option value="history">History</option>
-          </param>
-        <when value="cached">
-          <param name="normal_file" type="data" format="bam" label="Normal BAM file" >
-	    <validator type="unspecified_build" />
-            <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." />
-          </param>
-          <param name="tumor_file" type="data" format="bam" label="Tumor BAM file" >
-	    <validator type="unspecified_build" />
-            <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." />
-          </param>
-          <param name="ref_file" type="select" label="Using reference genome">
-            <options from_data_table="sam_fa_indexes">
-          </options>
-          </param>
-        </when>
-        <when value="history">
-          <param name="normal_file" type="data" format="bam" label="Normal BAM file" >
-            <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-          </param>
-          <param name="tumor_file" type="data" format="bam" label="Tumor BAM file" >
-            <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-          </param>
-          <param name="ref_file" type="data" format="fasta" label="Using reference file" />
-        </when>
-        </conditional>
-	<param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" />
-        <param name="disable_probabilistic_realignment" type="boolean" truevalue="-B" falsevalue="" checked="False" label="Disable probabilistic realignment for the computation of base alignment quality (BAQ)" />
-        <param name="max_reads_per_bam" type="integer" value="100000" label="Max reads per BAM" />
-        <param name="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for an alignment to be used" />
-        <param name="minimum_base_quality" type="integer" value="13" label="Minimum base quality for a base to be considered" />
-      </when>
-      <when value="pileup">
-        <param name="normal_file" type="data" format="pileup" label="Normal pileup file" />
-        <param name="tumor_file" type="data" format="pileup" label="Tumor pileup file" />
-      </when>
-      <when value="pileup_gz">
-        <param name="normal_file" type="data" format="pileup.gz" label="Normal pileup.gz file" />
-        <param name="tumor_file" type="data" format="pileup.gz" label="Tumor pileup.gz file" />
-      </when>
-    </conditional >
-    <param name="gc_content_file" type="data" format="txt" label="GC content file" />
-    <conditional name="usePersonalEstimation">
-      <param name="estimation" type="select" label="Do you want to use personal cellularity and ploidy? Otherwise Sequenza estimates cellularity and ploidy" >
-        <option value="no" selected="true">No</option>
-        <option value="yes" >Yes</option>
-      </param>
-      <when value="no" />
-      <when value="yes">
-        <param name="cellularity" type="integer" value="30" min="0" max="100" label="Cellularity used (%)" />
-        <param name="ploidy" type="integer" value="2" label="Ploidy used" />
-      </when>
-    </conditional >
-  </inputs>
-  <outputs>
-    <data format="html" name="HTMLFile" label="HTML output - Sequenza results" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="sampleName" value="test_curie"/>
-      <param name="fileFormat" value="pileup"/>
-      <param name="normal_file" value="constit_2.pileup"/>
-      <param name="tumor_file" value="tumor_2.pileup"/>
-      <param name="gc_content_file" value="hg19_chro1.gc50Base.txt"/>
-      <param name="estimation" value="yes"/>
-      <param name="cellularity" value="30"/>
-      <param name="ploidy" value="2"/>
-      <output name="HTMLFile" file="test_sequenza_1.dat" ftype="html"/>
-    </test>
-  </tests>
-  <help>
-
-**What it does**
-
-Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.
-
-  </help>
-  <citations>
-    <citation type="bibtex">@article{Favero01012015,
-      author = {Favero, F. and Joshi, T. and Marquard, A. M. and Birkbak, N. J. and Krzystanek, M. and Li, Q. and Szallasi, Z. and Eklund, A. C.},
-      title = {Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data},
-      volume = {26},
-      number = {1},
-      pages = {64-70},
-      year = {2015},
-      doi = {10.1093/annonc/mdu479},
-      URL = {http://annonc.oxfordjournals.org/content/26/1/64.abstract},
-      eprint = {http://annonc.oxfordjournals.org/content/26/1/64.full.pdf+html},
-      journal = {Annals of Oncology}
-      }</citation>
-    </citations>
-</tool>
--- a/tool_dependencies.xml	Fri Aug 21 05:46:18 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="fontconfig" version="2.11.1">
-      <repository changeset_revision="db378a241d59" name="package_fontconfig_2_11_1" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="python" version="2.7">
-      <repository changeset_revision="17b9d79ae892" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="sequenza" version="2.1.1">
-        <repository changeset_revision="fb754d87bb4e" name="package_r_sequenza_2_1_1" owner="jbrayet" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="samtools" version="1.2">
-        <repository changeset_revision="9cd278d52bb6" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>