Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 6:badd2d0f1689 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Mon, 10 Apr 2017 09:36:08 -0400
parents b52d29988df8
children 9e68bebb3d7c
comparison
equal deleted inserted replaced
5:b52d29988df8 6:badd2d0f1689
1 <tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="0.8.0"> 1 <tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.0">
2 <description>aligns gene family sequences</description> 2 <description>aligns gene family sequences</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements_gene_family_aligner" /> 6 <expand macro="requirements_gene_family_aligner" />
21 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit 21 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit
22 #end if 22 #end if
23 --num_threads \${GALAXY_SLOTS:-4} 23 --num_threads \${GALAXY_SLOTS:-4}
24 #if str($input_format) == 'ptortho': 24 #if str($input_format) == 'ptortho':
25 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 25 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
26 --output '$output_ptortho'
27 --output_dir '$output_ptortho.files_path'
28 #else: 26 #else:
29 ## str($input_format) == 'ptorthocs' 27 ## str($input_format) == 'ptorthocs'
30 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 28 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
31 #if str($input_format_cond.codon_alignments) == 'yes': 29 #if str($input_format_cond.codon_alignments) == 'yes':
32 --codon_alignments 'true' 30 --codon_alignments 'true'
33 --output '$output_ptorthocs'
34 --output_dir '$output_ptorthocs.files_path'
35 #else:
36 --output '$output_ptortho'
37 --output_dir '$output_ptortho.files_path'
38 #end if 31 #end if
39 #end if 32 #end if
40 #if str($options_type_cond.options_type) == 'advanced': 33 #if str($options_type_cond.options_type) == 'advanced':
41 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond 34 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond
42 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences 35 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
55 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of 48 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
56 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment 49 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
57 #end if 50 #end if
58 #end if 51 #end if
59 #end if 52 #end if
53 --output '$output'
54 --output_dir '$output.files_path'
60 ]]> 55 ]]>
61 </command> 56 </command>
62 <inputs> 57 <inputs>
63 <conditional name="input_format_cond"> 58 <conditional name="input_format_cond">
64 <param name="input_format" type="select" label="Select type of data to sub sample"> 59 <param name="input_format" type="select" label="Select type of data to sub sample">
86 <expand macro="cond_remove_gappy_sequences" /> 81 <expand macro="cond_remove_gappy_sequences" />
87 </when> 82 </when>
88 </conditional> 83 </conditional>
89 </inputs> 84 </inputs>
90 <outputs> 85 <outputs>
91 <data name="output_ptortho" format="ptortho" label="Aligned gene family sequences on ${on_string}"> 86 <data name="output" format="ptalign" label="Aligned gene family sequences on ${on_string}" />
92 <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')</filter>
93 </data>
94 <data name="output_ptorthocs" format="ptorthocs" label="Aligned gene family sequences and corresponding coding sequences on ${on_string}">
95 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes'</filter>
96 </data>
97 </outputs> 87 </outputs>
98 <tests> 88 <tests>
99 <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed. 89 <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.
100 <test> 90 <test>
101 </test> 91 </test>