# HG changeset patch
# User yhoogstrate
# Date 1446730158 18000
# Node ID 8544e51f79bbd77e673ff98e3e2a3eebfed0ba41
# Parent  a92c2ae342c447f5c78aeb279bc26246f2a3b39d
Deleted selected files

diff -r a92c2ae342c4 -r 8544e51f79bb samtools-parallel-mpileup.xml
--- a/samtools-parallel-mpileup.xml	Thu Nov 05 08:21:31 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,300 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="samtools_parallel_mpileup" name="Samtools parallel mpileup" version="0.1.19a.a">
-    <description>Samtools mpileup (supporting parallelization)</description>
-    
-    <requirements>
-        <requirement type="package" version="0.1.19a">samtools_parallel_mpileup_0_1_19a</requirement>
-        <requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement>
-    </requirements>
-    
-    <version_command>samtools 2&gt;&amp;1 | grep Version</version_command>
-    
-    <command>
-        #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
-            echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&amp;2
-        #else
-            #if $mpileup_parallelization.mpileup_parallelization_select == "true"
-                samtools-parallel-mpileup mpileup
-                -t $mpileup_parallelization.samtools_threads
-            #else
-                samtools mpileup
-            #end if
-                -f 
-                    #if $reference_genome_source.source_select == "indexed_filtered"
-                        "$reference_genome_source.reference_genome"
-                    #else if $reference_genome_source.source_select == "indexed_all"
-                        "$reference_genome_source.reference_genome"
-                    #else if $reference_genome_source.source_select == "history"
-                        "$reference_genome_source.reference_genome"
-                    #else
-                        <!--
-                            This is a workaround to obtain the "genome.fa" file that
-                            corresponds to the dbkey of the alignments.
-                            Because this file is "calculated" during run-time, it can
-                            be used in a workflow.
-                        -->
-                        "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
-                    #end if
-            
-            #if $extended_parameters_regions.samtools_regions == "region"
-                -r $extended_parameters_regions.$samtools_r
-            #elif $extended_parameters_regions.samtools_regions == "regions_file_pos" or $extended_parameters_regions.samtools_regions == "regions_file_bed"
-                -l $extended_parameters_regions.$samtools_l
-            #end if
-            
-            #if $extended_parameters.parameters == "extended"
-                $extended_parameters.samtools_6
-                $extended_parameters.samtools_A
-                $extended_parameters.samtools_B
-                 -C $extended_parameters.samtools_C
-                 -d $extended_parameters.samtools_d
-                $extended_parameters.samtools_E
-                 -M $extended_parameters.samtools_M
-                $extended_parameters.samtools_R
-                 -q $extended_parameters.samtools_q
-                 -Q $extended_parameters.samtools_Q
-                
-                 -e $extended_parameters.samtools_e
-                 -F $extended_parameters.samtools_F
-                 -h $extended_parameters.samtools_h
-                $extended_parameters.samtools_I
-                 -L $extended_parameters.samtools_L
-                 -m $extended_parameters.samtools_m
-                 -o $extended_parameters.samtools_o
-                $extended_parameters.samtools_p
-                 -P $extended_parameters.samtools_P
-            #end if
-            
-            #for $alignment in $alignments
-                 ${alignment}
-            #end for
-            
-             2> stderr_1.txt
-            
-            #if $sort_mpileup
-             | sort -k1,1V -k2,2g 
-            #end if
-            
-             > $output ;
-             cat stderr_1.txt
-        #end if
-    </command>
-    
-    <inputs>
-        <param format="bam,sam" multiple="true" name="alignments" type="data" label="Alignment file" help="Mapped reads in BAM or SAM format."/>
-        
-        <!-- Find out how to access the reference genome from the BAM file(s) -->
-        <conditional name="reference_genome_source">
-            <param name="source_select" type="select" label="Fasta Source">
-                <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
-                <option value="history">Use reference from the history</option>
-                <option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option>
-                <option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option>
-            </param>
-            <when value="indexed_filtered">
-                <param name="reference_genome" type="select" label="Reference Genome used during alignment (fasta)" >
-                    <options from_data_table="all_fasta">
-                        <column name="name" index="2"/>
-                        <column name="dbkey" index="1"/>
-                        <column name="value" index="3"/><!-- Value is the path of the fasta file -->
-                        <filter type="data_meta" ref="alignments" multiple="false" key="dbkey" column="1" />
-                        <validator type="no_options" message="No indexes are available for the selected input dataset" />
-                    </options>
-                </param>
-            </when>
-            <when value="history">
-                <param name="reference_genome" format="fasta" type="data" label="Reference Genome used during alignment (fasta)" help="Reference genome (genome.fa) that corresponds to the *.bam file." />
-            </when>
-            <when value="indexed_all">
-                <param name="reference_genome" type="select" label="Reference Genome used during alignment (fasta)" >
-                    <options from_data_table="all_fasta">
-                        <column name="name"  index="2"/>
-                        <column name="dbkey" index="1"/>
-                        <column name="value" index="3"/><!-- Value is the path of the fasta file -->
-                        <validator type="no_options" message="No indexes are available for the selected input dataset" />
-                    </options>
-                </param>
-            </when>
-            <when value="attribute" />
-        </conditional>
-        
-        <conditional name="extended_parameters_regions">
-            <param name="samtools_regions" type="select" label="Region specific parameters" help="Let samtools target specific genomic locations.">
-                <option value="entire_genome">Entire genome</option>
-                <option value="region">Specific region</option>
-                <option value="regions_file_pos">Specific positions (file); list of positions</option>
-                <option value="regions_file_bed">Specific regions (file); list of regions in BED</option>
-            </param>
-            <when value="entire_genome">
-            </when>
-            <when value="region">
-                <param type="text" name="samtools_r" label="Samtools: region in which pileup is generated" help="chr:pos or chr:start-end" />
-            </when>
-            <when value="regions_file_pos">
-                <param type="data" name="samtools_l" format="tabular" label="Samtools: list of positions (chr pos)" />
-            </when>
-            <when value="regions_file_bed">
-                <param type="data" name="samtools_l" format="bed"     label="Samtools: specific regions (BED)" />
-            </when>
-        </conditional>
-        
-        <conditional name="mpileup_parallelization">
-            <param name="mpileup_parallelization_select" type="select" label="Use parallelization for the mpileup generation (experimental)" help="Especially if larger numbers of bam/sam files are processed, or the file infrastructure is optimized for IO-paralellization, this feature might improve performance.">
-                <option value="false">False - uses classical samtools</option>
-                <option value="true">True - uses (experimental) samtools mpileup-parallel</option>
-            </param>
-            <when value="false" />
-            <when value="true">
-                <param type="integer" name="samtools_threads" value="2" min="1" label="Samtools: mpileup threads" />
-            </when>
-        </conditional>
-        
-        <param name="sort_mpileup" type="boolean" truevalue="true" falsevalue="false" label="Sort mpileup file" help="Because parallelization may disrupt the outputs order, sorting can be conveniet for e.g. testing. Notice that this function has only use in a limited number of situations but consumes (much) resources. Only use it if it's really neccesairy." />
-        
-        <conditional name="extended_parameters">
-            <param name="parameters" type="select" label="Advanced parameters" help="For more advanced VarScan and samtools settings.">
-                <option value="default">Default settings</option>
-                <option value="extended">Extended settings</option>
-            </param>
-            <when value="default" />
-            <when value="extended">
-                <param type="boolean" name="samtools_6" falsevalue="" truevalue=" -6" label="Samtools: assume the quality is in the Illumina-1.3+ encoding" />
-                <param type="boolean" name="samtools_A" falsevalue="" truevalue=" -A" label="Samtools: count anomalous read pairs" />
-                <param type="boolean" name="samtools_B" falsevalue="" truevalue=" -B" label="Samtools: disable BAQ computation" />
-                <param type="integer" name="samtools_C" value="0"                     label="Samtools: parameter for adjusting mapQ; 0 to disable [0]" />
-                <param type="integer" name="samtools_d" value="250"                   label="Samtools: max per-BAM depth to avoid excessive memory usage [250]" />
-                <param type="boolean" name="samtools_E" falsevalue="" truevalue=" -E" label="Samtools: recalculate extended BAQ on the fly thus ignoring existing BQs" />
-                <param type="integer" name="samtools_M" value="60"                    label="cap mapping quality at INT [60]" />
-                <param type="boolean" name="samtools_R" falsevalue="" truevalue=" -R" label="Samtools: ignore RG tags" />
-                <param type="integer" name="samtools_q" value="0"                     label="Samtools: skip alignments with mapQ smaller than INT [0]" />
-                <param type="integer" name="samtools_Q" value="13"                    label="Samtools: skip bases with baseQ/BAQ smaller than INT [13]" />
-                
-                <param type="integer" name="samtools_e" value="20"                    label="Samtools: Phred-scaled gap extension seq error probability [20]" />
-                <param type="float"   name="samtools_F" value="0.002"                 label="Samtools: minimum fraction of gapped reads for candidates [0.002]" help="Alias: -F" />
-                <param type="integer" name="samtools_h" value="100"                   label="Samtools: coefficient for homopolymer errors [100]" />
-                <param type="boolean" name="samtools_I" falsevalue="" truevalue=" -I" label="Samtools: do not perform indel calling" />
-                <param type="integer" name="samtools_L" value="250"                   label="Samtools: max per-sample depth for INDEL calling [250]" />
-                <param type="integer" name="samtools_m" value="1"                     label="Samtools: minimum gapped reads for indel candidates [1]" help="Alias: -m" />
-                <param type="integer" name="samtools_o" value="40"                    label="Samtools: Phred-scaled gap open sequencing error probability [40]" />
-                <param type="boolean" name="samtools_p" falsevalue="" truevalue=" -p" label="Samtools: apply -m and -F per-sample to increase sensitivity" />
-                <param type="text"    name="samtools_P" value="all"                   label="Samtools: comma separated list of platforms for indels [all]" />
-            </when>
-        </conditional>
-    </inputs>
-    
-    <outputs>
-        <data format="mpileup" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
-    </outputs>
-    
-    <tests>
-        <test><!-- Use classical samtools -->
-            <param name="alignments" value="example.bam" ftype="bam" />
-            
-            <param name="source_select" value="history" />
-            <param name="reference_genome" value="example.fa" ftypet="fasta" />
-            
-            <param name="samtools_regions" value="entire_genome" />
-            
-            <param name="mpileup_parallelization_select" value="false" />
-            <param name="sort_mpileup" value="true" />
-            
-            <param name="parameters" value="default" />
-            
-            
-            <output name="output" file="example.mpileup" /> 
-        </test>
-        <test><!-- Use parallelized samtools - @todo replace with sambamba! -->
-            <param name="alignments" value="example.bam" ftype="bam" />
-            
-            <param name="source_select" value="history" />
-            <param name="reference_genome" value="example.fa" ftypet="fasta" />
-            
-            <param name="samtools_regions" value="entire_genome" />
-            
-            <param name="mpileup_parallelization_select" value="true" />
-            <param name="samtools_threads" value="2" />
-            <param name="sort_mpileup" value="true" />
-            
-            <param name="parameters" value="default" />
-            
-            
-            <output name="output" file="example.mpileup.parallel" />
-        </test>
-    </tests>
-    
-    <help>
-**Samtools mpileup (supporting parallelization)**
-
-SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that:
-
-Is flexible enough to store all the alignment information generated by various alignment programs;
-Is simple enough to be easily generated by alignment programs or converted from existing alignment formats;
-Is compact in file size;
-Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory;
-Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus.
-SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
-
-SAMtools is hosted by SourceForge.net. The project page is http://samtools.sourceforge.net/. The source code releases are available from the download page. You can check out the most recent source code from the github project page with:
-git clone git://github.com/samtools/samtools.git 
-https://github.com/mydatascience/parallel-mpileup/
-
-Because samtools does not support parallization of the mpileup command, the project was forked to include paralellization support:
-
-
-However, since the project seems to lack support and contains fatal bugs this project was continued at:
-https://github.com/yhoogstrate/parallel-mpileup/
-
-
-**Input formats**
-
-Satmools accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/). The alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: *"database: hg19"* for a link to hg19, or *"database: ?"* if the link is missing.
-
-**Installation**
-
-The installation is fully automatic.
-
-**License**
-
-* parallel-mpileup: MIT License (https://github.com/yhoogstrate/parallel-mpileup/blob/master/samtools-0.1.19/COPYING)
-* samtool: MIT License
-
-
-Contact
--------
-
-The tool wrapper has been written by Youri Hoogstrate from the Erasmus
-Medical Center (Rotterdam, Netherlands) on behalf of the Translational
-Research IT (TraIT) project:
-
-http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
-
-More tools by the Translational Research IT (TraIT) project can be found
-in the following toolsheds:
-
-http://toolshed.dtls.nl/
-
-http://toolshed.g2.bx.psu.edu/
-
-http://testtoolshed.g2.bx.psu.edu/
-</help>
-    <citations>
-        <citation type="bibtex">
-           @unpublished{samtools_parallel_mpileup,
-              author       = {Youri Hoogstrate}, 
-              title        = { Samtools parallel-mpileup, fork of classical samtools },
-              year         = 2014,
-              url          = { https://github.com/yhoogstrate/parallel-mpileup }
-            }
-        </citation>
-        <citation type="bibtex">
-            @misc{SAM_def,
-            title={Definition of SAM/BAM format},
-            url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
-        </citation>
-        <citation type="bibtex">
-            @misc{SamTools_github,
-            title={SAMTools GitHub page},
-            url = {https://github.com/samtools/samtools},}
-        </citation>
-    </citations>
-</tool>
\ No newline at end of file