| Previous changeset 6:3a352cb57117 (2015-11-06) Next changeset 8:e9dcf64ef8ec (2015-11-06) |
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Commit message:
new option |
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modified:
vcf_to_snp.xml |
| b |
| diff -r 3a352cb57117 -r b617219a70b5 vcf_to_snp.xml --- a/vcf_to_snp.xml Fri Nov 06 15:12:17 2015 -0500 +++ b/vcf_to_snp.xml Fri Nov 06 15:17:20 2015 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="vcf_snp" name="vcf to snp" version="0.3"> +<tool id="vcf_snp" name="vcf to snp" version="0.5"> <description>vcf to snp for fasta</description> <requirements> <!-- Should just use the filter snp that's installed in the path --> @@ -8,21 +8,25 @@ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces ## ! We only have a simple single command here. - - <command interpreter="/usr/local/anaconda/bin/python"> + <command interpreter="python"> vcf_snp.py -s ${vcf} - -o output.txt + -p ${pos} + -o output.txt; + echo ${vcf.name} > name.txt; + cut -f2 output.txt >seq.txt; + paste name.txt seq.txt> output2.txt </command> <inputs> <param name="vcf" type="data" label="vcf" help=""/> + <param name="pos" type="data" label="positions" help=""/> </inputs> <outputs> - <data format="tabular" name="output_file" label="${vcf}" from_work_dir="output.txt"> + <data format="tabular" name="output_file" label="${vcf}" from_work_dir="output2.txt"> </data> </outputs> |