Mercurial > repos > iuc > ampvis2_heatmap

comparison heatmap.xml @ 8:c980e4bd48f2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9fe04d29ea604a152144908dbd20c0754695a025
author iuc
date Sat, 16 Nov 2024 19:58:32 +0000
parents 14695ae019be
children
comparison
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7:9dab85e62cf2 8:c980e4bd48f2
1 <tool id="ampvis2_heatmap" name="ampvis2 heatmap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> 1 <tool id="ampvis2_heatmap" name="ampvis2 heatmap" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="header"/> 6 <expand macro="header"/>
61 normalise_by = "$normalise_by", 61 normalise_by = "$normalise_by",
62 #end if 62 #end if
63 #if $scale_by 63 #if $scale_by
64 scale_by = "$scale_by", 64 scale_by = "$scale_by",
65 #end if 65 #end if
66 ## color_vector = NULL 66 color_vector = c("$color_palette_start", "$color_palette_end"),
67 ## round = 1, 67 ## round = 1,
68 #if $output_options.out_format == "tabular" 68 #if $output_options.out_format == "tabular"
69 textmap = TRUE, 69 textmap = TRUE,
70 #else 70 #else
71 textmap = FALSE, 71 textmap = FALSE,
148 <filter type="unique_value" column="1"/> 148 <filter type="unique_value" column="1"/>
149 </options> 149 </options>
150 </param> 150 </param>
151 </when> 151 </when>
152 </conditional> 152 </conditional>
153 <param argument="color_palette_start" type="color" label="Start color for the heatmap" help="Choose the start color for the heatmap."/>
154 <param argument="color_palette_end" type="color" label="End color for the heatmap" help="Choose the end color for the heatmap."/>
153 <!-- https://github.com/KasperSkytte/ampvis2/issues/168 155 <!-- https://github.com/KasperSkytte/ampvis2/issues/168
154 if this is possible again reuse: metadata_sample_or_variable_select ? --> 156 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"/> 157 <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"/> 158 <expand macro="metadata_select_discrete" argument="scale_by" label="Scale the abundances by a variable in the metadata"/>
157 159
292 <param name="function_data" value="AalborgWWTPs-functions.tsv" ftype="tsv"/> 294 <param name="function_data" value="AalborgWWTPs-functions.tsv" ftype="tsv"/>
293 <param name="functions" value="Foo,Bar"/> 295 <param name="functions" value="Foo,Bar"/>
294 </conditional> 296 </conditional>
295 <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_file.pdf" ftype="pdf" compare="sim_size"/> 297 <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_file.pdf" ftype="pdf" compare="sim_size"/>
296 </test> 298 </test>
299 <!-- test with different color palettes -->
300 <test expect_num_outputs="1">
301 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
302 <param name="color_palette_start" value="red"/>
303 <param name="color_palette_end" value="yellow"/>
304 <output name="plot" value="AalborgWWTPs-heatmap-red-yellow.pdf" ftype="pdf" compare="sim_size"/>
305 </test>
306 <test expect_num_outputs="1">
307 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
308 <param name="color_palette_start" value="blue"/>
309 <param name="color_palette_end" value="green"/>
310 <output name="plot" value="AalborgWWTPs-heatmap-blue-green.pdf" ftype="pdf" compare="sim_size"/>
311 </test>
297 312
298 </tests> 313 </tests>
299 <help><![CDATA[ 314 <help><![CDATA[
300 What it does 315 What it does
301 ============ 316 ============