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Updated Bowtie test files to handle new version (0.12.3) of Bowtie (bowtie_color_wrapper will fail until new version installed). Updated samtools tools test files. Removed version references from Bowtie and BWA tools.

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This commit is contained in:
Kelly Vincent
2010-02-24 07:11:43 -05:00
parent a28313bb46
commit 09fa3f0bf1
7 changed files with 31 additions and 37 deletions
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test-data/sam_to_bam_out1.bam
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tools/samtools/sam_merge.xml
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<tool id="sam_merge" name="Merge BAM Files" version="1.0.0">
<tool id="sam_merge" name="Merge BAM Files" version="1.1.0">
<description>merges BAM files together</description>
<command interpreter="python">
sam_merge.py
tools/samtools/sam_pileup.xml
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@@ -1,4 +1,4 @@
<tool id="sam_pileup" name="Generate pileup" version="1.0.0">
<tool id="sam_pileup" name="Generate pileup" version="1.1.0">
<description>from BAM dataset</description>
<command interpreter="python">
sam_pileup.py
tools/samtools/sam_to_bam.xml
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@@ -1,4 +1,4 @@
<tool id="sam_to_bam" name="SAM-to-BAM" version="1.0.0">
<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.0">
<description>converts SAM format to BAM format</description>
<command interpreter="python">
sam_to_bam.py --input1=$source.input1 --dbkey=${input1.metadata.dbkey}
tools/sr_mapping/bowtie_color_wrapper.xml
+14 -16
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@@ -197,12 +197,12 @@
<option value="history">Use one from the history</option>
</param>
<when value="indexed">
<param name="index" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team">
<options from_file="bowtie_indices_color.loc">
<column name="value" index="1" />
<column name="name" index="0" />
</options>
</param>
<param name="index" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team">
<options from_file="bowtie_indices_color.loc">
<column name="value" index="1" />
<column name="name" index="0" />
</options>
</param>
</when>
<when value="history">
<param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
@@ -252,7 +252,7 @@
</when> <!-- cIndexFull -->
</conditional> <!-- cIndexParams -->
</when> <!-- cHistory -->
</conditional> <!-- cRefGenomeSource -->
</conditional> <!-- cRefGenomeSource -->
<conditional name="singlePaired">
<param name="sPaired" type="select" label="Is this library mate-paired?">
<option value="single">Single-end</option>
@@ -262,9 +262,9 @@
<param name="sInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
<conditional name="sParams">
<param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
<option value="preSet">Commonly used</option>
<option value="full">Full parameter list</option>
</param>
<option value="preSet">Commonly used</option>
<option value="full">Full parameter list</option>
</param>
<when value="preSet" />
<when value="full">
<param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
@@ -327,9 +327,9 @@
</param>
<conditional name="pParams">
<param name="pSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
<option value="preSet">Commonly used</option>
<option value="full">Full parameter list</option>
</param>
<option value="preSet">Commonly used</option>
<option value="full">Full parameter list</option>
</param>
<when value="preSet" />
<when value="full">
<param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />
@@ -417,7 +417,7 @@
<!--
Bowtie command:
bowtie-build -f -C test-data/chr_m.fasta chrM_color
bowtie -X 1000 +ff -n 2 -e 70 -l 28 -X 250 +ff +pairtries 100 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color -1 test-data/bowtie_in3.fastqsanger -2 test-data/bowtie_in4.fastqsanger > test-data/bowtie_out3.sam
bowtie -X 1000 +ff -n 2 -e 70 -l 28 -X 250 +pairtries 100 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color -1 test-data/bowtie_in3.fastqsanger -2 test-data/bowtie_in4.fastqsanger > test-data/bowtie_out3.sam
-p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
chrM_base is the index files' location/base name.
-->
@@ -533,8 +533,6 @@
Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
This tool uses Bowtie version 0.12.1.
.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
------
tools/sr_mapping/bowtie_wrapper.xml
+14 -16
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@@ -191,13 +191,13 @@
<option value="history">Use one from the history</option>
</param>
<when value="indexed">
<param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
<options from_file="bowtie_indices.loc">
<column name="value" index="1" />
<column name="name" index="0" />
</options>
</param>
</when>
<param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
<options from_file="bowtie_indices.loc">
<column name="value" index="1" />
<column name="name" index="0" />
</options>
</param>
</when>
<when value="history">
<param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
<conditional name="indexParams">
@@ -246,7 +246,7 @@
</when> <!-- indexFull -->
</conditional> <!-- indexParams -->
</when> <!-- history -->
</conditional> <!-- refGenomeSource -->
</conditional> <!-- refGenomeSource -->
<conditional name="singlePaired">
<param name="sPaired" type="select" label="Is this library mate-paired?">
<option value="single">Single-end</option>
@@ -256,9 +256,9 @@
<param name="sInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
<conditional name="sParams">
<param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
<option value="preSet">Commonly used</option>
<option value="full">Full parameter list</option>
</param>
<option value="preSet">Commonly used</option>
<option value="full">Full parameter list</option>
</param>
<when value="preSet" />
<when value="full">
<param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
@@ -315,9 +315,9 @@
</param>
<conditional name="pParams">
<param name="pSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
<option value="preSet">Commonly used</option>
<option value="full">Full parameter list</option>
</param>
<option value="preSet">Commonly used</option>
<option value="full">Full parameter list</option>
</param>
<when value="preSet" />
<when value="full">
<param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />
@@ -506,8 +506,6 @@
Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
This tool uses Bowtie version 0.12.1.
.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
------
tools/sr_mapping/bwa_wrapper.xml
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@@ -181,8 +181,6 @@
BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome. It is developed by Heng Li at the Sanger Insitute. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-60.
This tool uses BWA version 0.5.5.
------
**Know what you are doing**