Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 32:14af615b80b4 draft

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Uploaded
author greg
date Mon, 22 May 2017 15:19:10 -0400
parents 4d6e5f90aab8
children e58f6138188c
comparison
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31:5691bc0a32d2 32:14af615b80b4
100 </when> 100 </when>
101 </conditional> 101 </conditional>
102 <expand macro="cond_remove_gappy_sequences" /> 102 <expand macro="cond_remove_gappy_sequences" />
103 </inputs> 103 </inputs>
104 <outputs> 104 <outputs>
105 <data name="output_aln" format="ptalign" label="Aligned gene family sequences on ${on_string}"> 105 <data name="output_aln" format="ptalign" label="${tool.name} (aligned gene family sequences) on ${on_string}">
106 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter> 106 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
107 </data> 107 </data>
108 <data name="output_aln_ca" format="ptalignca" label="Aligned gene family sequences with codon alignments on ${on_string}"> 108 <data name="output_aln_ca" format="ptalignca" label="${tool.name} (aligned gene family sequences with codon alignments) on ${on_string}">
109 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter> 109 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
110 </data> 110 </data>
111 <data name="output_aln_filtered" format="ptalignfiltered" label="Filtered aligned gene family sequences on ${on_string}"> 111 <data name="output_aln_filtered" format="ptalignfiltered" label="${tool.name} (filtered aligned gene family sequences) on ${on_string}">
112 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter> 112 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter>
113 </data> 113 </data>
114 <data name="output_aln_filtered_ca" format="ptalignfilteredca" label="Filtered aligned gene family sequences with codon alignments on ${on_string}"> 114 <data name="output_aln_filtered_ca" format="ptalignfilteredca" label="${tool.name} (filtered aligned gene family sequences with codon alignments) on ${on_string}">
115 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter> 115 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter>
116 </data> 116 </data>
117 <data name="output_aln_trimmed" format="ptaligntrimmed" label="Trimmed aligned gene family sequences on ${on_string}"> 117 <data name="output_aln_trimmed" format="ptaligntrimmed" label="${tool.name} (trimmed aligned gene family sequences) on ${on_string}">
118 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter> 118 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
119 </data> 119 </data>
120 <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="Trimmed aligned gene family sequences with codon alignments on ${on_string}"> 120 <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="${tool.name} (trimmed aligned gene family sequences with codon alignments) on ${on_string}">
121 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter> 121 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
122 </data> 122 </data>
123 </outputs> 123 </outputs>
124 <tests> 124 <tests>
125 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed. 125 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.