Mercurial > repos > yhoogstrate > crossmap
changeset 16:263581d4dd90 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
| author | yhoogstrate |
|---|---|
| date | Thu, 13 Aug 2015 10:19:19 -0400 |
| parents | 22a09104afcc |
| children | a2ca0062cded |
| files | crossmap.xml test-data/test_bam_01_output_a.sam test-data/test_bigwig_01_input_a.bw test-data/test_bigwig_01_output_a.bw test-data/test_bigwig_01_output_a.sorted.bgr test-data/test_wig_01_input_a.wig test-data/test_wig_01_output_a.bw test-data/test_wig_01_output_a.sorted.bgr tool_dependencies.xml |
| diffstat | 9 files changed, 62 insertions(+), 16 deletions(-) [+] |
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--- a/crossmap.xml Thu Aug 13 07:52:11 2015 -0400 +++ b/crossmap.xml Thu Aug 13 10:19:19 2015 -0400 @@ -2,16 +2,17 @@ <description>Convert genome coordinates or annotation files between genome assemblies</description> <requirements> + <requirement type="package" version="312">ucsc_tools</requirement> <requirement type="package" version="0.2">crossmap</requirement> </requirements> - <version_command>CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command> - <stdio> <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/> <regex match=".*" source="both" level="log"/> </stdio> - + + <version_command>CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command> + <command> CrossMap.py ${multiple.input_format.replace("sam","bam")} @@ -47,6 +48,9 @@ #else if $multiple.input_format in ["vcf"] ; mv "${output}" "$output" ; mv "${output}.unmap" "$output_unmapped" + #else if $multiple.input_format in ["wig", "bigwig"] + ; mv "${output}.bw" "$output" + ; mv "${output}.sorted.bgr" "$output2" #end if </command> @@ -178,6 +182,8 @@ <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> </when> </conditional> + + <param name="include_fails" type="hidden" tvalue="False" /> </when> <when value="gff"> <conditional name="seq_source"> @@ -290,6 +296,8 @@ <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> </when> </conditional> + + <param name="include_fails" type="hidden" tvalue="False" /> </when> </conditional> </inputs> @@ -303,7 +311,7 @@ <when input="multiple.input_format" value="bigwig" format="bigwig" /> <when input="multiple.input_format" value="gff" format="gff" /> <when input="multiple.input_format" value="vcf" format="vcf" /> - <when input="imultiple.nput_format" value="wig" format="wig" /> + <when input="imultiple.nput_format" value="wig" format="bigwig" /> </change_format> </data> @@ -311,11 +319,13 @@ <filter>input_format in ["bam" , "vcf"]</filter> <change_format> <when input="multiple.input_format" value="bam" format="bam" /> - <when input="multiple.input_format" value="sam" format="sam" /> - <when input="multiple.input_format" value="bigwig" format="bigwig" /> - <when input="multiple.input_format" value="gff" format="gff" /> <when input="multiple.input_format" value="vcf" format="vcf" /> - <when input="multiple.input_format" value="wig" format="wig" /> + </change_format> + </data> + <data format="text" name="output2" label="${tool.name} on "> + <filter>input_format in ["wig"]</filter> + <change_format> + <when input="multiple.input_format" value="wig" format="bedgraph" /> </change_format> </data> </outputs> @@ -371,15 +381,24 @@ <output name="output" file="test_bed_02_output_a__all.bed"/> </test> - <!-- BigWig --> - + <!-- BigWig --><!-- Malfuncioning in CrossMap 0.2 + <test> + <param name="input_format" value="bigwig"/> + <param name="index_source" value="history"/> + <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/> + <param name="input_chain" value="aToB.over.chain" ftype="csv"/> + <param name="include_fails" value="False"/> + + <output name="output" file="test_bigwig_01_output_a.bw"/> + <output name="output2" file="test_bigwig_01_output_a.sorted.bgr"/> + </test>--> <!-- GFF --> <test> <param name="input_format" value="gff"/> <param name="index_source" value="history"/> <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> <param name="input_chain" value="aToB.over.chain" ftype="csv"/> - <param name="include_fails" value="false"/> + <param name="include_fails" value="False"/> <output name="output" file="test_gff_01_output_a__only-matches.gtf"/> </test> @@ -388,7 +407,7 @@ <param name="index_source" value="history"/> <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> <param name="input_chain" value="aToB.over.chain" ftype="csv"/> - <param name="include_fails" value="true"/> + <param name="include_fails" value="True"/> <output name="output" file="test_gff_01_output_a__all.gtf"/> </test> @@ -405,10 +424,19 @@ <output name="output" file="test_vcf_01_output.vcf" compare="diff" lines_diff="4"/> <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/> </test> - - <!-- WIG --> </tests> - + + <!-- WIG - Doesn't understand fixedStep --> + <test> + <param name="input_format" value="wig"/> + <param name="index_source" value="history"/> + <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/> + <param name="input_chain" value="aToB.over.chain" ftype="csv"/> + <param name="include_fails" value="False"/> + + <output name="output" file="test_wig_01_output_a.bw"/> + <output name="output2" file="test_wig_01_output_a.sorted.bgr"/> + </test> <help> CrossMap is versatile tool to convert genome coordinates or annotation files between genome assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
--- a/test-data/test_bam_01_output_a.sam Thu Aug 13 07:52:11 2015 -0400 +++ b/test-data/test_bam_01_output_a.sam Thu Aug 13 10:19:19 2015 -0400 @@ -5,7 +5,7 @@ @SQ SN:chr3 LN:199501827 @SQ SN:chr4 LN:191273063 @PG ID:- VN:1.0.0 CL:cmatrix -@PG ID:CrossMap VN:0.1.10 +@PG ID:CrossMap VN:0.2 @CO Test data for CrossMap bam @CO Liftover from original BAM/SAM file: @CO Liftover is based on the chain file:
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bigwig_01_output_a.sorted.bgr Thu Aug 13 10:19:19 2015 -0400 @@ -0,0 +1,3 @@ +chr1 889863 989862 110.0 +chr2 890000 989999 220.0 +chr3 875000 974999 330.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_wig_01_input_a.wig Thu Aug 13 10:19:19 2015 -0400 @@ -0,0 +1,10 @@ +variableStep chrom=chr1 span=900000 +100000 110 +variableStep chrom=chr2 span=900000 +100000 220 +variableStep chrom=chr3 span=900000 +100000 330 +variableStep chrom=chr4 span=50000 +9200000 400 +variableStep chrom=chr4 span=60000 +8940000 450
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_wig_01_output_a.sorted.bgr Thu Aug 13 10:19:19 2015 -0400 @@ -0,0 +1,2 @@ +chr2 89999 989999 220.0 +chr3 74999 974999 330.0
--- a/tool_dependencies.xml Thu Aug 13 07:52:11 2015 -0400 +++ b/tool_dependencies.xml Thu Aug 13 10:19:19 2015 -0400 @@ -1,5 +1,8 @@ <?xml version="1.0"?> <tool_dependency> + <package name="ucsc_tools" version="312"><!-- For conversion of Wig and BigWig --> + <repository changeset_revision="34e9010db346" name="package_ucsc_tools_312" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> <package name="crossmap" version="0.2"> <repository changeset_revision="1aa7754d9c75" name="package_crossmap_0_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package>