Mercurial > repos > iuc > ampvis2_heatmap

comparison heatmap.xml @ 3:a2d4da20749a 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 07:53:13 +0000
parents 1adde216bdce
children 14695ae019be
comparison
equal deleted inserted replaced
2:1adde216bdce 3:a2d4da20749a
55 max_abundance = $max_abundance, 55 max_abundance = $max_abundance,
56 #end if 56 #end if
57 #if $sort_by_cond.sort_by_sel != 'no' 57 #if $sort_by_cond.sort_by_sel != 'no'
58 sort_by = "$sort_by_cond.sort_by", 58 sort_by = "$sort_by_cond.sort_by",
59 #end if 59 #end if
60 ## TODO https://github.com/MadsAlbertsen/ampvis2/issues/130 60 #if $normalise_by
61 ## #if $normalise_by_cond.normalise_by_sel != "no" 61 normalise_by = "$normalise_by",
62 ## normalise_by = "$normalise_by_cond.normalise_by", 62 #end if
63 ## #end if
64 #if $scale_by 63 #if $scale_by
65 scale_by = "$scale_by", 64 scale_by = "$scale_by",
66 #end if 65 #end if
67 ## color_vector = NULL 66 ## color_vector = NULL
68 ## round = 1, 67 ## round = 1,
149 <filter type="unique_value" column="1"/> 148 <filter type="unique_value" column="1"/>
150 </options> 149 </options>
151 </param> 150 </param>
152 </when> 151 </when>
153 </conditional> 152 </conditional>
154 <!-- TODO https://github.com/MadsAlbertsen/ampvis2/issues/130 --> 153 <!-- https://github.com/KasperSkytte/ampvis2/issues/168
155 <!-- <expand macro="metadata_sample_select" argument="normalise_by" label="Normalize counts by a variable or a specific sample"/> --> 154 if this is possible again reuse: metadata_sample_or_variable_select ? -->
155 <expand macro="metadata_sample_select" argument="normalise_by" label="Normalize counts by a variable or a specific sample"/>
156 <expand macro="metadata_select_discrete" argument="scale_by" label="Scale the abundances by a variable in the metadata"/> 156 <expand macro="metadata_select_discrete" argument="scale_by" label="Scale the abundances by a variable in the metadata"/>
157 157
158 <conditional name="plot_functions_cond"> 158 <conditional name="plot_functions_cond">
159 <param name="plot_functions_sel" type="select" label="Show functional information about the Genus-level OTUs" help="Produces a 2-column grid plot, showing known functional information about the Genus-level OTUs next to the heatmap. When using this feature, make sure that either tax_aggregate or tax_add is set to Genus and that Genus is the lowest level in either."> 159 <param name="plot_functions_sel" type="select" label="Show functional information about the Genus-level OTUs" help="Produces a 2-column grid plot, showing known functional information about the Genus-level OTUs next to the heatmap. When using this feature, make sure that either tax_aggregate or tax_add is set to Genus and that Genus is the lowest level in either.">
160 <option value="no">No</option> 160 <option value="no">No</option>
224 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 224 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
225 <param name="normalise" value="true"/> 225 <param name="normalise" value="true"/>
226 <output name="plot" value="AalborgWWTPs-heatmap-normalise.pdf" ftype="pdf"/> 226 <output name="plot" value="AalborgWWTPs-heatmap-normalise.pdf" ftype="pdf"/>
227 </test> 227 </test>
228 <!-- normalise by a specific sample --> 228 <!-- normalise by a specific sample -->
229 <!-- TODO https://github.com/MadsAlbertsen/ampvis2/issues/130 --> 229 <test expect_num_outputs="1">
230 <!-- <test expect_num_outputs="1">
231 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 230 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
232 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 231 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
233 <param name="normalise" value="true"/> 232 <param name="normalise" value="true"/>
234 <conditional name="normalise_by_cond"> 233 <param name="normalise_by" value="16SAMP-747"/>
235 <param name="normalise_by_sel" value="sample"/>
236 <param name="normalise_by" value="16SAMP-747"/>
237 </conditional>
238 <output name="plot" value="AalborgWWTPs-heatmap-normalise_by_sample.pdf" ftype="pdf"/> 234 <output name="plot" value="AalborgWWTPs-heatmap-normalise_by_sample.pdf" ftype="pdf"/>
239 </test> --> 235 </test>
240 <!-- normalise by a metadata variable --> 236 <!-- normalise by a metadata variable
241 <!-- TODO https://github.com/MadsAlbertsen/ampvis2/issues/130 --> 237 https://github.com/KasperSkytte/ampvis2/issues/168 -->
242 <!-- <test expect_num_outputs="1"> 238 <!-- <test expect_num_outputs="1">
243 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 239 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
244 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 240 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
245 <param name="group_by" value="Plant"/> 241 <param name="group_by" value="Plant"/>
246 <conditional name="normalise_by_cond"> 242 <conditional name="normalise_by_cond">