changeset 64:76fb170b2697 draft

Deleted selected files

--- a/picard_ReorderSam.xml	Tue Feb 18 16:34:54 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,158 +0,0 @@
-<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.106.0">
-<!-- taken from Inserthttps://github.com/najoshi/ucd-biocore-galaxy/tree/master/tools/picard -->
-  <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
-  <command interpreter="python">
-    picard_wrapper.py
-      --input=$inputFile
-      #if $source.indexSource == "built-in"
-        --ref="${source.ref.fields.path}"
-      #else
-        --ref-file=$refFile
-        --species-name=$source.speciesName
-        --build-name=$source.buildName
-        --trunc-names=$source.truncateSeqNames
-      #end if
-      --allow-inc-dict-concord=$allowIncDictConcord
-      --allow-contig-len-discord=$allowContigLenDiscord
-      --output-format=$outputFormat
-      --output=$outFile
-      --tmpdir "${__new_file_path__}"
-      -j "\$JAVA_JAR_PATH/ReorderSam.jar"
-  </command>
-  <inputs>
-    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered"
-           help="If empty, upload or import a SAM/BAM dataset." />
-    <conditional name="source">
-      <param name="indexSource" type="select" label="Select Reference Genome" help="This tool will re-order SAM/BAM in the same order as reference selected below.">
-        <option value="built-in">Locally cached</option>
-        <option value="history">History</option>
-      </param>
-      <when value="built-in">
-        <param name="ref" type="select" label="Select a reference genome">
-          <options from_data_table="picard_indexes" />
-        </param>
-      </when>
-      <when value="history">
-        <param name="refFile" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
-        <param name="speciesName" type="text" value="" label="Species name" />
-        <param name="buildName" type="text" value="" label="Build name" />
-        <param name="truncateSeqNames" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Truncate sequence names after first whitespace" />
-      </when>
-    </conditional>
-    <param name="allowIncDictConcord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow incomplete dict concordance?" help="Allows a partial overlap of the BAM contigs with the new reference sequence contigs." />
-    <param name="allowContigLenDiscord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow contig length discordance?" help="This is dangerous--don't check it unless you know exactly what you're doing!" />
-    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
-  </inputs>
-  <outputs>
-    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: reordered ${outputFormat}">
-      <change_format>
-        <when input="outputFormat" value="sam" format="sam" />
-      </change_format>
-    </data>
-  </outputs>
-  <tests>
-    <test>
-      <!-- Commands:
-cp test-data/phiX.fasta .
-samtools faidx phiX.fasta
-java -jar CreateSequenceDictionary.jar R=phiX.fasta O=phiX.dict URI=phiX.fasta TRUNCATE_NAMES_AT_WHITESPACE=false SPECIES=phiX174
-java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input1.bam O=picard_RS_output1.bam REFERENCE=phiX.fasta ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false
--->
-      <param name="inputFile" value="picard_RS_input1.bam" />
-      <param name="indexSource" value="history" />
-      <param name="refFile" value="phiX.fasta" />
-      <param name="speciesName" value="phiX174" />
-      <param name="buildName" value="" />
-      <param name="truncateSeqNames" value="false" />
-      <param name="allowIncDictConcord" value="false" />
-      <param name="allowContigLenDiscord" value="false" />
-      <param name="outputFormat" value="True" />
-      <output name="outFile" file="picard_RS_output1.bam" ftype="bam" lines_diff="4" compare="contains" />
-    </test>
-    <test>
-      <!-- Command:
-java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input2.sam O=picard_RS_output2.sam REFERENCE=/path/to/phiX/picard_index/phiX.fa ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false
-/path/to/phiX/srma_index/phiX.fa is path to phiX.fa, phiX.fa.fai, and phiX.dict
--->
-      <param name="inputFile" value="picard_RS_input2.sam" />
-      <param name="indexSource" value="built-in" />
-      <param name="ref" value="phiX" />
-      <param name="allowIncDictConcord" value="false" />
-      <param name="allowContigLenDiscord" value="false" />
-      <param name="outputFormat" value="False" />
-      <output name="outFile" file="picard_RS_output2.sam" ftype="sam" lines_diff="4" sort="True" />
-    </test>
-    <test>
-      <!-- Commands:
-cp test-data/picard_RS_input4.fasta .
-samtools faidx picard_RS_input4.fasta
-java -jar CreateSequenceDictionary.jar R=picard_RS_input4.fasta O=picard_RS_input4.dict URI=picard_RS_input4.fasta TRUNCATE_NAMES_AT_WHITESPACE=true SPECIES=phiX174 GENOME_ASSEMBLY=phiX_buildBlah1.1
-java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input3.bam O=picard_RS_output3.sam REFERENCE=picard_RS_input4.fasta ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false
-picard_RS_input3.bam can be made from picard_RS_input3.sam
--->
-      <param name="inputFile" value="picard_RS_input3.bam" />
-      <param name="indexSource" value="history" />
-      <param name="refFile" value="picard_RS_input4.fasta" />
-      <param name="speciesName" value="phiX174" />
-      <param name="buildName" value="phiX_buildBlah1.1" />
-      <param name="truncateSeqNames" value="true" />
-      <param name="allowIncDictConcord" value="true" />
-      <param name="allowContigLenDiscord" value="false" />
-      <param name="outputFormat" value="False" />
-      <output name="outFile" file="picard_RS_output3.sam" ftype="sam" lines_diff="12" sort="True" />
-    </test>
-  </tests>
-  <help>
-
-.. class:: infomark
-
-**Purpose**
-
-Reorder SAM/BAM to match contig ordering in a particular reference file. Note that this is
-not the same as sorting as done by the SortSam tool, which sorts by either coordinate
-values or query name. The ordering in ReorderSam is based on exact name matching of
-contigs/chromosomes. Reads that are mapped to a contig that is not in the new reference file are
-not included in the output.
-
-**Picard documentation**
-
-This is a Galaxy wrapper for ReorderSam, a part of the external package Picard-tools_.
-
- .. _Picard-tools: http://www.google.com/search?q=picard+samtools
-
-------
-
-.. class:: infomark
-
-**Inputs, outputs, and parameters**
-
-For the file that needs to be reordered, either a sam file or a bam file must be supplied.
-If a bam file is used, it must be coordinate-sorted. A reference file is also required,
-so either a fasta file should be supplied or a built-in reference can be selected.
-
-The output contains the same reads as the input file but the reads have been rearranged so
-they appear in the same order as the provided reference file. The tool will output either
-bam (the default) or sam, according to user selection. Bam is recommended since it is smaller.
-
-The only extra parameters that can be set are flags for allowing incomplete dict concordance
-and allowing contig length discordance. If incomplete dict concordance is allowed, only a
-partial overlap of the bam contigs with the new reference sequence contigs is required. By
-default it is off, requiring a corresponding contig in the new reference for each read contig.
-If contig length discordance is allowed, contig names that are the same between a read and the
-new reference contig are allowed even if they have different lengths. This is usually not a
-good idea, unless you know exactly what you're doing. It's off by default.
-
-.. class:: warningmark
-
-**Warning on SAM/BAM quality**
-
-Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
-flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
-to be the only way to deal with SAM/BAM that cannot be parsed.
-
-
-  </help>
-</tool>
-
-
-