Mercurial > repos > iuc > ampvis2_subset_taxa

comparison macros.xml @ 3:512e102a19ad draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
author iuc
date Mon, 26 Feb 2024 07:51:07 +0000
parents 1332619ad9ec
children e2df49914652
comparison
equal deleted inserted replaced
2:1332619ad9ec 3:512e102a19ad
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">2.7.22</token> 2 <token name="@TOOL_VERSION@">2.8.6</token>
3 <token name="@VERSION_SUFFIX@">1</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">22.01</token> 4 <token name="@PROFILE@">22.01</token>
5 <xml name="header"> 5 <xml name="header">
6 <xrefs> 6 <xrefs>
7 <xref type="bio.tools">ampvis</xref> 7 <xref type="bio.tools">ampvis</xref>
8 </xrefs> 8 </xrefs>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">r-ampvis2</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">r-ampvis2</requirement>
11 <requirement type="package" version="2.1.1">r-readr</requirement> 11 <requirement type="package" version="2.1.5">r-readr</requirement>
12 <requirement type="package" version="1.46.0">bioconductor-phyloseq</requirement>
12 </requirements> 13 </requirements>
13 <version_command><![CDATA[ 14 <version_command><![CDATA[
14 echo $(R --version | grep "R version")", ampvis2 version" $(R --vanilla --slave -e "library(ampvis2, quietly = TRUE); sessionInfo()\$otherPkgs\$ampvis2\$Version" 2> /dev/null | grep -v -i "WARNING: ") 15 echo $(R --version | grep "R version")", ampvis2 version" $(R --vanilla --slave -e "library(ampvis2, quietly = TRUE); sessionInfo()\$otherPkgs\$ampvis2\$Version" 2> /dev/null | grep -v -i "WARNING: ")
15 ]]></version_command> 16 ]]></version_command>
16 17
34 </xml> 35 </xml>
35 36
36 <token name="@SAVE_TAX_LIST@"><![CDATA[ 37 <token name="@SAVE_TAX_LIST@"><![CDATA[
37 for(level in colnames(data\$tax)){ 38 for(level in colnames(data\$tax)){
38 for(u in unique(data\$tax[level])){ 39 for(u in unique(data\$tax[level])){
39 write(u, file="$taxonomy_list_out", append=T) 40 write(paste(u, level, sep="\t"), file="$taxonomy_list_out", append=T)
40 } 41 }
41 } 42 }
42 ]]></token> 43 ]]></token>
43 44
44 <token name="@SAVE_METADATA_LIST@"><![CDATA[ 45 <token name="@SAVE_METADATA_LIST@"><![CDATA[
150 </token> 151 </token>
151 <yield/> 152 <yield/>
152 </expand> 153 </expand>
153 </xml> 154 </xml>
154 155
156 <!-- metadata_sample_or_variable_select is currently unused (heatmap is documented to allow normalize by
157 sample or variable, but only sample seems possible https://github.com/KasperSkytte/ampvis2/issues/168
158 leaving it for now in case it can be fixed .. then metadata_sample_select could be removed) -->
155 <xml name="metadata_sample_select" token_argument=""> 159 <xml name="metadata_sample_select" token_argument="">
160 <param argument="@ARGUMENT@" type="select" optional="true">
161 <options from_dataset="metadata_list">
162 <column name="name" index="1"/>
163 <column name="value" index="1"/>
164 <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples -->
165 <filter type="unique_value" column="1"/>
166 </options>
167 </param>
168 </xml>
169 <xml name="metadata_sample_or_variable_select" token_argument="">
156 <conditional name="@ARGUMENT@_cond"> 170 <conditional name="@ARGUMENT@_cond">
157 <param name="@ARGUMENT@_sel" type="select"> 171 <param name="@ARGUMENT@_sel" type="select">
158 <option value="no">No</option> 172 <option value="no">No</option>
159 <option value="variable">Metadata variable</option> 173 <option value="variable">Metadata variable</option>
160 <option value="sample">Specific sample</option> 174 <option value="sample">Specific sample</option>
162 <when value="no"/> 176 <when value="no"/>
163 <when value="variable"> 177 <when value="variable">
164 <expand macro="metadata_select" argument="@ARGUMENT@" label="Metadata variable"/> 178 <expand macro="metadata_select" argument="@ARGUMENT@" label="Metadata variable"/>
165 </when> 179 </when>
166 <when value="sample"> 180 <when value="sample">
167 <param argument="@ARGUMENT@" type="select" optional="true"> 181 <expand macro="metadata_sample_select"/>
168 <options from_dataset="metadata_list">
169 <column name="name" index="1"/>
170 <column name="value" index="1"/>
171 <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples -->
172 <filter type="unique_value" column="1"/>
173 </options>
174 </param>
175 </when> 182 </when>
176 </conditional> 183 </conditional>
177 </xml> 184 </xml>
178 185
179 <xml name="taxonomy_select_macro" token_argument="" token_optional="false" token_multiple="true"> 186 <xml name="taxonomy_select_macro" token_argument="" token_optional="false" token_multiple="true">