Mercurial > repos > yhoogstrate > crossmap
diff crossmap.xml @ 7:1efce8a693ca draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
| author | yhoogstrate |
|---|---|
| date | Thu, 12 Nov 2015 16:08:56 -0500 |
| parents | 5ef4ac8f2956 |
| children |
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--- a/crossmap.xml Thu Nov 12 10:42:27 2015 -0500 +++ b/crossmap.xml Thu Nov 12 16:08:56 2015 -0500 @@ -14,7 +14,8 @@ <version_command>python $CROSSMAP_ROOT_DIR/bin/CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command> - <command><!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: --> + <!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: --> + <command><![CDATA[ python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py ${multiple.input_format.replace("sam","bam")} @@ -44,16 +45,16 @@ "$output" #if $multiple.input_format in ["bam", "sam"] - ; mv "${output}.${multiple.input_format}" "$output" - ; mv "${output}.unmap.${multiple.input_format}" "$output_unmapped" + && mv "${output}.${multiple.input_format}" "$output" + && mv "${output}.unmap.${multiple.input_format}" "$output_unmapped" #else if $multiple.input_format in ["vcf"] - ; mv "${output}" "$output" - ; mv "${output}.unmap" "$output_unmapped" + && mv "${output}" "$output" + && mv "${output}.unmap" "$output_unmapped" #else if $multiple.input_format in ["wig", "bigwig"] - ; mv "${output}.bw" "$output" - ; mv "${output}.sorted.bgr" "$output2" + && mv "${output}.bw" "$output" + && mv "${output}.sorted.bgr" "$output2" #end if - </command> + ]]></command> <inputs> <conditional name="multiple"> @@ -73,7 +74,7 @@ <option value="history">From History</option> </param> <when value="cached"> - <param type="data" format="bam" name="input" label="BAM/SAM file"> + <param type="data" format="bam" name="input" label="BAM file"> <validator type="unspecified_build" /> <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> </param> @@ -105,7 +106,7 @@ <option value="history">From History</option> </param> <when value="cached"> - <param type="data" format="sam" name="input" label="BAM/SAM file"> + <param type="data" format="sam" name="input" label="SAM file"> <validator type="unspecified_build" /> <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> </param> @@ -334,6 +335,17 @@ <tests> <!-- BAM/SAM --> <test> + <param name="input_format" value="bam"/> + <param name="index_source" value="history"/> + <param name="input" value="test_bam_01_input_a.sam" ftype="bam"/> + <param name="input_chain" value="aToB.over.chain" ftype="csv"/> + <param name="include_fails" value="False"/> + + <output name="output" file="test_bam_01_output_a.sam" compare="diff" lines_diff="4"/> + <output name="output_unmapped" file="test_bam_01_output_a.unmap.sam"/> + </test> + + <test> <param name="input_format" value="sam"/> <param name="index_source" value="history"/> <param name="input" value="test_bam_01_input_a.sam" ftype="sam"/>