# HG changeset patch
# User yhoogstrate
# Date 1447342240 18000
# Node ID ebcd672e9072795fc5fe5de9b41ca5c459dd7c4a
# Parent 179bf64d12ef08c36fec8b3e904d1e2792a0d2c0
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
diff -r 179bf64d12ef -r ebcd672e9072 crossmap.xml
--- a/crossmap.xml Thu Nov 12 10:26:25 2015 -0500
+++ b/crossmap.xml Thu Nov 12 10:30:40 2015 -0500
@@ -16,127 +16,270 @@
python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py
- ${input_format.replace("sam","bam")}
+ ${multiple.input_format.replace("sam","bam")}
- #if $input_format == "vcf" and $seq_source.index_source == "cached"
+ #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached"
- "${filter(lambda x: str( x[1] ) == str($seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
+ "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
#else
- "$seq_source.input_chain"
+ "$multiple.seq_source.input_chain"
#end if
- #if $input_format in ["bam", "sam"]
- -m $insert_size
- -s $insert_size_stdev
- -t $insert_size_fold
+ #if $multiple.input_format in ["bam", "sam"]
+ -m $multiple.insert_size
+ -s $multiple.insert_size_stdev
+ -t $multiple.insert_size_fold
#end if
- "$seq_source.input"
+ "$multiple.seq_source.input"
- #if $input_format == "vcf"
- "$seq_source.input_fasta"
+ #if $multiple.input_format == "vcf"
+ "$multiple.seq_source.input_fasta"
#end if
- #if str($include_fails) == "True"
+ #if str($multiple.include_fails) == "True"
>
#end if
"$output"
- #if $input_format in ["bam", "sam"]
- ; mv "${output}.${input_format}" "$output"
- ; mv "${output}.unmap.${input_format}" "$output_unmapped"
- #else if $input_format in ["vcf"]
+ #if $multiple.input_format in ["bam", "sam"]
+ ; mv "${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"
- #else if $input_format in ["wig", "bigwig"]
+ #else if $multiple.input_format in ["wig", "bigwig"]
; mv "${output}.bw" "$output"
; mv "${output}.sorted.bgr" "$output2"
#end if
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input_format in ["bam" , "vcf"]
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input_format in ["wig"]
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