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comparison tools/ncbi_blast_plus/blastxml_to_tabular.xml @ 20:c5f20ca77de2 draft

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planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit de1ad30e756a7073c422d5677fe5c6750521fa1b-dirty
author peterjc
date Wed, 26 Apr 2017 06:47:08 -0400
parents 1039cd165d92
children 771b554bc85d
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19:a212d2984601 20:c5f20ca77de2
1 <tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="@WRAPPER_VERSION@"> 1 <tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="@WRAPPER_VERSION@">
2 <description>Convert BLAST XML output to tabular</description> 2 <description>Convert BLAST XML output to tabular</description>
3 <macros> 3 <macros>
4 <import>ncbi_macros.xml</import> 4 <import>ncbi_macros.xml</import>
5 </macros> 5 </macros>
6 <stdio> 6 <version_command>python $__tool_directory__/blastxml_to_tabular.py --version</version_command>
7 <!-- Anything other than zero is an error --> 7 <command detect_errors="aggressive">
8 <exit_code range="1:" /> 8 python $__tool_directory__/blastxml_to_tabular.py -o '$tabular_file'
9 <exit_code range=":-1" />
10 </stdio>
11 <version_command interpreter="python">blastxml_to_tabular.py --version</version_command>
12 <command interpreter="python">
13 blastxml_to_tabular.py -o "$tabular_file"
14 #if $output.out_format == "cols": 9 #if $output.out_format == "cols":
15 #set cols = (str($output.std_cols)+","+str($output.ext_cols)).replace("None", " ").replace(",,", ",").replace(",", " ") 10 #set cols = (str($output.std_cols)+","+str($output.ext_cols)).replace("None", " ").replace(",,", ",").replace(",", " ")
16 -c "$cols" 11 -c '$cols'
17 #else 12 #else
18 -c "$output.out_format" 13 -c '$output.out_format'
19 #end if 14 #end if
20 #for i in $blastxml_file#"${i}" #end for# 15 #for i in $blastxml_file#'${i}' #end for#
21 </command> 16 </command>
22 <inputs> 17 <inputs>
23 <param name="blastxml_file" type="data" format="blastxml" multiple="true" label="BLAST results as XML"/> 18 <param name="blastxml_file" type="data" format="blastxml" multiple="true" label="BLAST results as XML"/>
24 <conditional name="output"> 19 <conditional name="output">
25 <param name="out_format" type="select" label="Output format"> 20 <param name="out_format" type="select" label="Output format">