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comparison macros.xml @ 1:47bfbd6597d0 draft

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planemo upload commit 636fd1c7e60779d1123056a2985d54881013d4cb
author galaxyp
date Wed, 05 Dec 2018 14:37:17 -0500
parents b17b03126d40
children 80ce9ca55697
comparison
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0:b17b03126d40 1:47bfbd6597d0
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="@VERSION@">metaquantome</requirement> 5 <requirement type="package" version="@VERSION@">metaquantome</requirement>
6 <yield/> 6 <yield/>
7 </requirements> 7 </requirements>
8 </xml>
9 <xml name="ONTOLOGY_ARGS">
10 <conditional name="ontology_args">
11 <param name="ontology" type="select" label="Ontology">
12 <option value="go">GO Gene Ontology (column named 'go')</option>
13 <option value="ec">EC Enzyme Commission (column named 'ec')</option>
14 <option value="cog">COG (column named 'cog')</option>
15 </param>
16 <when value="go">
17 <param argument="--slim_down" type="boolean" label="Use slim GO"/>
18 </when>
19 <when value="ec">
20 <!-- do nothing -->
21 </when>
22 <when value="cog">
23 <!-- do nothing -->
24 </when>
25 </conditional>
8 </xml> 26 </xml>
9 <xml name="FUNC_FILE"> 27 <xml name="FUNC_FILE">
10 <param argument="--func_file" type="data" format="tabular" label="Functional file" 28 <param argument="--func_file" type="data" format="tabular" label="Functional file"
11 help="Tabular file with a peptide sequence column and a functional assignment column for GO-term, EC number, or COG."/> 29 help="Tabular file with a peptide sequence column and a functional assignment column for GO-term, EC number, or COG."/>
12 <param argument="--pep_colname_func" type="text" label="Peptide column name" 30 <param argument="--pep_colname_func" type="text" label="Peptide column name"
48 #end if 66 #end if
49 ]]> 67 ]]>
50 </token> 68 </token>
51 <token name="@DB_DIR@"><![CDATA[ 69 <token name="@DB_DIR@"><![CDATA[
52 #if $db_dir.db_loc == 'auto': 70 #if $db_dir.db_loc == 'auto':
53 #if $mode_args.mode == 'taxfn' 71 #if $mode_args.mode == 'ft'
54 --ft_func_data_dir data 72 --ft_func_data_dir data
55 --ft_tax_data_dir data 73 --ft_tax_data_dir data
56 #else 74 #else
57 --data_dir data 75 --data_dir data
58 #end if 76 #end if
83 </xml> 101 </xml>
84 <token name="@COMMON_PARAMS@"><![CDATA[ 102 <token name="@COMMON_PARAMS@"><![CDATA[
85 --samps samp_file.tab 103 --samps samp_file.tab
86 --mode '$mode_args.mode' 104 --mode '$mode_args.mode'
87 #if $mode_args.mode == 'f' 105 #if $mode_args.mode == 'f'
106 --ontology='$mode_args.ontology_args.ontology'
107 #if $mode_args.ontology_args.ontology == 'go'
108 #if $mode_args.ontology_args.slim_down
109 --slim_down
110 #end if
111 #end if
112 #end if
113 #if $mode_args.mode == 'ft'
114 --ontology='$mode_args.ontology_args.ontology'
115 #if $mode_args.ontology_args.ontology == 'go'
116 #if $mode_args.ontology_args.slim_down
117 --slim_down
118 #end if
119 #end if
120 #end if
121 ]]>
122 </token>
123 <token name="@EXPAND_PARAMS@"><![CDATA[
124 --samps samp_file.tab
125 --mode '$mode_args.mode'
126 #if $mode_args.mode == 'f'
88 --func_file='$mode_args.func_file' 127 --func_file='$mode_args.func_file'
89 --func_colname='$mode_args.func_colname' 128 --func_colname='$mode_args.func_colname'
90 --pep_colname_func='$mode_args.pep_colname_func' 129 --pep_colname_func='$mode_args.pep_colname_func'
91 --ontology='$mode_args.ontology_args.ontology' 130 --ontology='$mode_args.ontology_args.ontology'
92 #if $mode_args.ontology_args.ontology == 'go' 131 #if $mode_args.ontology_args.ontology == 'go'
102 #end if 141 #end if
103 #if $mode_args.mode == 'ft' 142 #if $mode_args.mode == 'ft'
104 --func_file='$mode_args.func_file' 143 --func_file='$mode_args.func_file'
105 --func_colname='$mode_args.func_colname' 144 --func_colname='$mode_args.func_colname'
106 --pep_colname_func='$mode_args.pep_colname_func' 145 --pep_colname_func='$mode_args.pep_colname_func'
107 --ontology=$mode_args.ontology 146 --ontology='$mode_args.ontology_args.ontology'
147 #if $mode_args.ontology_args.ontology == 'go'
148 #if $mode_args.ontology_args.slim_down
149 --slim_down
150 #end if
151 #end if
108 --tax_file='$mode_args.tax_file' 152 --tax_file='$mode_args.tax_file'
109 --tax_colname='$mode_args.tax_colname' 153 --tax_colname='$mode_args.tax_colname'
110 --pep_colname_tax='$mode_args.pep_colname_tax' 154 --pep_colname_tax='$mode_args.pep_colname_tax'
111 --ft_tar_rank='$mode_args.ft_tar_rank' 155 --ft_tar_rank='$mode_args.ft_tar_rank'
112 #end if 156 #end if
113 ]]> 157 ]]>
114 </token> 158 </token>
159
115 <xml name="SAMPS"> 160 <xml name="SAMPS">
116 <conditional name="samps_args"> 161 <conditional name="samps_args">
117 <param argument="samps_src" type="select" label="Samples"> 162 <param argument="samps_src" type="select" label="Samples">
118 <option value="history">Use a samples dataset from your history</option> 163 <option value="history">Use a samples dataset from your history</option>
119 <option value="build">Specify samples</option> 164 <option value="build">Specify samples</option>
136 <option value="f">Functional analysis</option> 181 <option value="f">Functional analysis</option>
137 <option value="t">Taxonomic analysis</option> 182 <option value="t">Taxonomic analysis</option>
138 <option value="ft">Functional-taxonomic interaction analysis</option> 183 <option value="ft">Functional-taxonomic interaction analysis</option>
139 </param> 184 </param>
140 <when value="f"> 185 <when value="f">
186 <expand macro="ONTOLOGY_ARGS"/>
187 </when>
188 <when value="t">
189 </when>
190 <when value="ft">
191 <expand macro="ONTOLOGY_ARGS"/>
192 </when>
193 </conditional>
194 <expand macro="SAMPS"/>
195 </xml>
196 <xml name="expand_params">
197 <conditional name="mode_args">
198 <param argument="--mode" type="select" label="Mode">
199 <option value="f">Functional analysis</option>
200 <option value="t">Taxonomic analysis</option>
201 <option value="ft">Functional-taxonomic interaction analysis</option>
202 </param>
203 <when value="f">
141 <expand macro="FUNC_FILE"/> 204 <expand macro="FUNC_FILE"/>
142 <conditional name="ontology_args"> 205 <expand macro="ONTOLOGY_ARGS"/>
143 <param name="ontology" type="select" label="Ontology">
144 <option value="go">GO Gene Ontology (column named 'go')</option>
145 <option value="ec">EC Enzyme Commission (column named 'ec')</option>
146 <option value="cog">COG (column named 'cog')</option>
147 </param>
148 <when value="go">
149 <param argument="--slim_down" type="boolean" label="Use slim GO"/>
150 </when>
151 <when value="ec">
152 <!-- do nothing -->
153 </when>
154 <when value="cog">
155 <!-- do nothing -->
156 </when>
157 </conditional>
158 </when> 206 </when>
159 <when value="t"> 207 <when value="t">
160 <expand macro="TAX_FILE"/> 208 <expand macro="TAX_FILE"/>
161 </when> 209 </when>
162 <when value="ft"> 210 <when value="ft">
163 <expand macro="FUNC_FILE"/> 211 <expand macro="FUNC_FILE"/>
212 <expand macro="ONTOLOGY_ARGS"/>
164 <expand macro="TAX_FILE"/> 213 <expand macro="TAX_FILE"/>
165 <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy"> 214 <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy">
166 <option value="species">species</option> 215 <option value="species">species</option>
167 <option value="genus" selected="true">genus</option> 216 <option value="genus" selected="true">genus</option>
168 <option value="family">family</option> 217 <option value="family">family</option>
173 </param> 222 </param>
174 </when> 223 </when>
175 </conditional> 224 </conditional>
176 <expand macro="SAMPS"/> 225 <expand macro="SAMPS"/>
177 </xml> 226 </xml>
227
178 <xml name="output_samples_choice"> 228 <xml name="output_samples_choice">
179 <param name="output_samps" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output the samples fiile"/> 229 <param name="output_samps" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output the samples fiile"/>
180 </xml> 230 </xml>
181 <xml name="output_samples"> 231 <xml name="output_samples">
182 <data format="tabular" name="samples_file" label="${tool.name} on ${on_string} samples" from_work_dir="samp_file.tab"> 232 <data format="tabular" name="samples_file" label="${tool.name} on ${on_string} samples" from_work_dir="samp_file.tab">