Mercurial > repos > jjohnson > contig_annotation_tool

comparison macros.xml @ 3:18ece3d5bcde draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 3febcc9ba3d3717877c36bf96742209012a13ac4-dirty
author jjohnson
date Tue, 26 Nov 2019 15:42:14 -0500
parents 9a01840eac52
children aaeb63501369
comparison
equal deleted inserted replaced
2:9a01840eac52 3:18ece3d5bcde
17 <option value="cached">local cached database</option> 17 <option value="cached">local cached database</option>
18 <option value="history">history</option> 18 <option value="history">history</option>
19 </param> 19 </param>
20 <when value="cached"> 20 <when value="cached">
21 <param name="cat_builtin" type="select" label="Use a built-in CAT database" help="If the CAT database of interest is not listed, contact your Galaxy administrator"> 21 <param name="cat_builtin" type="select" label="Use a built-in CAT database" help="If the CAT database of interest is not listed, contact your Galaxy administrator">
22 <options from_data_table="cat_databases"> 22 <options from_data_table="cat_database">
23 <filter type="sort_by" column="2" /> 23 <filter type="sort_by" column="2" />
24 <validator type="no_options" message="No CAT database is available." /> 24 <validator type="no_options" message="No CAT database is available." />
25 </options> 25 </options>
26 </param> 26 </param>
27 </when> 27 </when>
75 --proteins_fasta '$previous.proteins_fasta' 75 --proteins_fasta '$previous.proteins_fasta'
76 --diamond_alignment '$previous.diamond_alignment' 76 --diamond_alignment '$previous.diamond_alignment'
77 #end if 77 #end if
78 --out_prefix 'cat_output' 78 --out_prefix 'cat_output'
79 ]]></token> 79 ]]></token>
80
81 <xml name="custom_settings"> 80 <xml name="custom_settings">
82 <param argument="--range" type="integer" value="10" min="0" max="49" label="range"/> 81 <param argument="--range" type="integer" value="10" min="0" max="49" label="range"/>
83 <param argument="--fraction" type="float" value="0.5" min="0" max="0.99" label="fraction"/> 82 <param argument="--fraction" type="float" value="0.5" min="0" max="0.99" label="fraction"/>
84 </xml> 83 </xml>
85 <token name="@CUSTOM_SETTINGS@"><![CDATA[ 84 <token name="@CUSTOM_SETTINGS@"><![CDATA[
113 <when value="both"> 112 <when value="both">
114 <expand macro="add_names_options"/> 113 <expand macro="add_names_options"/>
115 </when> 114 </when>
116 </conditional> 115 </conditional>
117 </xml> 116 </xml>
117 <token name="@TXT2TSV@">${__tool_directory__}/tabpad.py</token>
118 <token name="@ADD_NAMES@"><![CDATA[ 118 <token name="@ADD_NAMES@"><![CDATA[
119 #if $names.add_names in ['classification','both']: 119 #if $names.add_names in ['classification','both']:
120 && CAT add_names $names.only_official $names.exclude_scores 120 && CAT add_names $names.only_official $names.exclude_scores
121 @CAT_TAXONOMY@ 121 @CAT_TAXONOMY@
122 #if $bcat == 'CAT' 122 #if $bcat == 'CAT'
123 -i cat_output.contig2classification.tsv 123 -i cat_output.contig2classification.tsv
124 #else 124 #else
125 -i cat_output.bin2classification.tsv 125 -i cat_output.bin2classification.tsv
126 #end if 126 #end if
127 -o classification_names.txt 127 -o classification_names.txt
128 && @TXT2TSV@ -i classification_names.txt -o $classification_names 128 && ${__tool_directory__}/tabpad.py -i classification_names.txt -o $classification_names
129 #end if 129 #end if
130 #if $names.add_names in ['orf2lca','both']: 130 #if $names.add_names in ['orf2lca','both']:
131 && CAT add_names $names.only_official $names.exclude_scores 131 && CAT add_names $names.only_official $names.exclude_scores
132 @CAT_TAXONOMY@ 132 @CAT_TAXONOMY@
133 -i cat_output.ORF2LCA.tsv 133 -i cat_output.ORF2LCA.tsv
134 -o orf2lca_names.txt 134 -o orf2lca_names.txt
135 && @TXT2TSV@ -i orf2lca_names.txt -o $orf2lca_names 135 && ${__tool_directory__}/tabpad.py -i orf2lca_names.txt -o $orf2lca_names
136 #end if 136 #end if
137 ]]></token> 137 ]]></token>
138 <xml name="summarise"> 138 <xml name="summarise">
139 <param name="summarise" type="select" label="summarise"> 139 <param name="summarise" type="select" label="summarise">
140 <option value="no">No</option> 140 <option value="no">No</option>
160 #if $bcat == 'CAT' 160 #if $bcat == 'CAT'
161 -c $contigs_fasta 161 -c $contigs_fasta
162 #end if 162 #end if
163 -i $summary_input 163 -i $summary_input
164 -o classification_summary.txt 164 -o classification_summary.txt
165 && @TXT2TSV@ -i classification_summary.txt -o $classification_summary 165 && ${__tool_directory__}/tabpad.py -i classification_summary.txt -o $classification_summary
166 #end if 166 #end if
167 ]]></token> 167 ]]></token>
168 168
169 <xml name="select_outputs"> 169 <xml name="select_outputs">
170 <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs"> 170 <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs">
192 <param name="bin_col" type="hidden" value="bin,"/> 192 <param name="bin_col" type="hidden" value="bin,"/>
193 <expand macro="select_outputs"> 193 <expand macro="select_outputs">
194 <option value="bin2classification" selected="true">bin2classification.txt</option> 194 <option value="bin2classification" selected="true">bin2classification.txt</option>
195 </expand> 195 </expand>
196 </xml> 196 </xml>
197
198 <token name="@TXT2TSV@"><![CDATA[
199 $__tool_directory__/tabpad.py
200 ]]></token>
201 <xml name="outputs"> 197 <xml name="outputs">
202 <data name="log" format="txt" label="${bcat}.log" from_work_dir="cat_output.log"> 198 <data name="log" format="txt" label="${bcat}.log" from_work_dir="cat_output.log">
203 <filter>'log' in select_outputs or not select_outputs</filter> 199 <filter>'log' in select_outputs or not select_outputs</filter>
204 </data> 200 </data>
205 <data name="predicted_proteins_faa" format="fasta" label="${bcat}.predicted_proteins.faa" from_work_dir="cat_output.predicted_proteins.faa"> 201 <data name="predicted_proteins_faa" format="fasta" label="${bcat}.predicted_proteins.faa" from_work_dir="cat_output.predicted_proteins.faa">
263 ]]></token> 259 ]]></token>
264 <xml name="citations"> 260 <xml name="citations">
265 <citations> 261 <citations>
266 <citation type="doi">https://doi.org/10.1101/072868</citation> 262 <citation type="doi">https://doi.org/10.1101/072868</citation>
267 <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation> 263 <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation>
264 <citation type="doi">https://doi.org/10.1038/nmeth.3176</citation>
265 <citation type="doi">https://doi.org/10.1186/1471-2105-11-119</citation>
268 <yield /> 266 <yield />
269 </citations> 267 </citations>
270 </xml> 268 </xml>
271 </macros> 269 </macros>