# HG changeset patch
# User yhoogstrate
# Date 1447341985 18000
# Node ID 179bf64d12ef08c36fec8b3e904d1e2792a0d2c0
# Parent 871455bebf64e238358907d1734b145de37ad055
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
diff -r 871455bebf64 -r 179bf64d12ef crossmap.xml
--- a/crossmap.xml Thu Nov 12 10:13:37 2015 -0500
+++ b/crossmap.xml Thu Nov 12 10:26:25 2015 -0500
@@ -16,270 +16,127 @@
python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py
- ${multiple.input_format.replace("sam","bam")}
+ ${input_format.replace("sam","bam")}
- #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached"
+ #if $input_format == "vcf" and $seq_source.index_source == "cached"
- "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
+ "${filter(lambda x: str( x[1] ) == str($seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
#else
- "$multiple.seq_source.input_chain"
+ "$seq_source.input_chain"
#end if
- #if $multiple.input_format in ["bam", "sam"]
- -m $multiple.insert_size
- -s $multiple.insert_size_stdev
- -t $multiple.insert_size_fold
+ #if $input_format in ["bam", "sam"]
+ -m $insert_size
+ -s $insert_size_stdev
+ -t $insert_size_fold
#end if
- "$multiple.seq_source.input"
+ "$seq_source.input"
- #if $multiple.input_format == "vcf"
- "$multiple.seq_source.input_fasta"
+ #if $input_format == "vcf"
+ "$seq_source.input_fasta"
#end if
- #if str($multiple.include_fails) == "True"
+ #if str($include_fails) == "True"
>
#end if
"$output"
- #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"]
+ #if $input_format in ["bam", "sam"]
+ ; mv "${output}.${input_format}" "$output"
+ ; mv "${output}.unmap.${input_format}" "$output_unmapped"
+ #else if $input_format in ["vcf"]
; mv "${output}" "$output"
; mv "${output}.unmap" "$output_unmapped"
- #else if $multiple.input_format in ["wig", "bigwig"]
+ #else if $input_format in ["wig", "bigwig"]
; mv "${output}.bw" "$output"
; mv "${output}.sorted.bgr" "$output2"
#end if
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- multiple.input_format in ["bam" , "vcf"]
+ input_format in ["bam" , "vcf"]
-
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- multiple.input_format in ["wig"]
+ input_format in ["wig"]
-
+