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Updated sam-to-bam to properly assign output dbkey; enhanced sam-to-bam and bam-to-sam functional tests

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This commit is contained in:
Kelly Vincent
2011-05-09 12:00:05 -04:00
parent db5d90222e
commit 772da79c12
3 changed files with 44 additions and 25 deletions
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tools/samtools/bam_to_sam.xml
+14 -11
View File
@@ -1,4 +1,4 @@
<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.2">
<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.3">
<requirements>
<requirement type="package">samtools</requirement>
</requirements>
@@ -20,29 +20,32 @@
<test>
<!--
Bam-to-Sam command:
samtools view -o bam_to_sam_out1.sam test-data/3unsorted.bam
samtools view -o bam_to_sam_out1.sam test-data/bam_to_sam_in1.bam
bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
-->
<param name="input1" value="1.bam" ftype="bam" />
<param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
<param name="header" value="" />
<output name="output1" file="bam_to_sam_out1.sam" sorted="True" />
<param name="header" value="" />
</test>
<test>
<!--
Bam-to-Sam command:
samtools view -o bam_to_sam_out2.sam test-data/1.bam
samtools view -o bam_to_sam_out2.sam test-data/bam_to_sam_in2.bam
bam_to_sam_in2.bam can be created from bam_to_sam_in2.sam
-->
<param name="input1" value="3unsorted.bam" ftype="bam" />
<param name="input1" value="bam_to_sam_in2.bam" ftype="bam" />
<param name="header" value="" />
<output name="output1" file="bam_to_sam_out2.sam" sorted="True" />
<param name="header" value="" />
</test>
<test>
<!--
Bam-to-Sam command:
samtools view -h -o bam_to_sam_out1.sam test-data/1.bam
samtools view -h -o bam_to_sam_out3.sam test-data/bam_to_sam_in1.bam
bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
-->
<param name="input1" value="1.bam" ftype="bam" />
<output name="output1" file="bam_to_sam_out3.sam" sorted="True" />
<param name="header" value="True" />
<param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
<param name="header" value="--header" />
<output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /><!-- header param not working in func tests so won't produce correct 6-line header (fine in browser) -->
</test>
</tests>
<help>
tools/samtools/sam_to_bam.py
+1 -1
View File
@@ -68,7 +68,7 @@ def __main__():
# and the equCab2.fa file will contain fasta sequences.
seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file )
tmp_dir = tempfile.mkdtemp()
if options.ref_file == 'None':
if not options.ref_file or options.ref_file == 'None':
# We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ).
# The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in
# a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai
tools/samtools/sam_to_bam.xml
+29 -13
View File
@@ -1,4 +1,4 @@
<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.1">
<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.2">
<description>converts SAM format to BAM format</description>
<requirements>
<requirement type="package">samtools</requirement>
@@ -6,11 +6,11 @@
<command interpreter="python">
sam_to_bam.py
--input1=$source.input1
--dbkey=${input1.metadata.dbkey}
#if $source.index_source == "history":
--dbkey=${ref_file.metadata.dbkey}
--ref_file=$source.ref_file
#else
--ref_file="None"
--dbkey=${input1.metadata.dbkey}
#end if
--output1=$output1
--index_dir=${GALAXY_DATA_INDEX_DIR}
@@ -22,44 +22,60 @@
<option value="history">History</option>
</param>
<when value="cached">
<param name="input1" type="data" format="sam" label="SAM File to Convert">
<param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert">
<validator type="unspecified_build" />
<validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" />
</param>
</when>
<when value="history">
<param name="input1" type="data" format="sam" label="Convert SAM file" />
<param name="ref_file" type="data" format="fasta" label="Using reference file" />
<param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
</when>
</conditional>
</inputs>
<outputs>
<data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM" />
<data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM">
<actions>
<conditional name="source.index_source">
<when value="cached">
<action type="metadata" name="dbkey">
<option type="from_param" name="source.input1" param_attribute="dbkey" />
</action>
</when>
<when value="history">
<action type="metadata" name="dbkey">
<option type="from_param" name="source.ref_file" param_attribute="dbkey" />
</action>
</when>
</conditional>
</actions>
</data>
</outputs>
<tests>
<test>
<!--
Sam-to-Bam command:
cp test-data/chr_m.fasta .
samtools faidx chr_m.fasta
samtools view -bt chr_m.fasta.fai -o unsorted.bam test-data/3.sam
samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam
samtools sort unsorted.bam sam_to_bam_out1
chr_m.fasta is the reference file
chr_m.fasta is the reference file (chrM from equCab2)
-->
<param name="index_source" value="history" />
<param name="input1" value="3.sam" ftype="sam" />
<param name="input1" value="sam_to_bam_in1.sam" ftype="sam" />
<param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" />
<output name="output1" file="sam_to_bam_out1.bam" />
<output name="output1" file="sam_to_bam_out1.bam" ftype="bam" />
</test>
<test>
<!--
Sam-to-Bam command:
samtools view -bt chr_m.fasta.fai -o unsorted.bam test-data/3.sam
samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam
samtools sort unsorted.bam sam_to_bam_out2
chr_m.fasta is the reference file and the index chr_m.fasta.fai
should be in the same directory
these should be in the same directory, and chrM is from equCab2
-->
<param name="index_source" value="cached" />
<param name="input1" value="3.sam" ftype="sam" dbkey="equCab2" />
<param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" />
<output name="output1" file="sam_to_bam_out2.bam" ftype="bam" />
</test>
</tests>