Mercurial > repos > galaxyp > metaquantome_viz

comparison metaquantome_viz.xml @ 1:8c30496a665a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
author galaxyp
date Wed, 23 Sep 2020 17:01:47 +0000
parents 6cfd42b015b4
children 02da24eac445
comparison
equal deleted inserted replaced
0:6cfd42b015b4 1:8c30496a665a
29 </xml> 29 </xml>
30 <xml name="common_volc_params"> 30 <xml name="common_volc_params">
31 <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe"> 31 <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe">
32 <validator type="empty_field"/> 32 <validator type="empty_field"/>
33 </param> 33 </param>
34 <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe">
35 <validator type="empty_field"/>
36 </param>
34 <param argument="--textannot" type="text" optional="true" label="Name of the annotation column" 37 <param argument="--textannot" type="text" optional="true" label="Name of the annotation column"
35 help="Provides text annotatation for the plot. Optional. If missing, no text will be plotted."/> 38 help="Provides text annotatation for the plot. Optional. If missing, no text will be plotted."/>
36 <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false" 39 <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false"
37 label="Flip the fold change (i.e., multiply log fold change by -1)"/> 40 label="Flip the fold change (i.e., multiply log fold change by -1)"/>
38 </xml> 41 </xml>
42 label="Only plot significant term" help="Necessitates use of results from `test`"/> 45 label="Only plot significant term" help="Necessitates use of results from `test`"/>
43 <when value="true"> 46 <when value="true">
44 <param argument="--alpha" type="float" 47 <param argument="--alpha" type="float"
45 value="0.05" min="0.0" max="1.0" 48 value="0.05" min="0.0" max="1.0"
46 label="The q-value significance level"/> 49 label="The q-value significance level"/>
50 <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe">
51 <validator type="empty_field"/>
52 </param>
47 </when> 53 </when>
48 <when value="false"> 54 <when value="false">
49 <!-- do nothing --> 55 <!-- do nothing -->
50 </when> 56 </when>
51 </conditional> 57 </conditional>
58 <param argument="--feature_cluster_size" type="integer" label="For tabular output. Number of clusters 'k' to cut the feature dendrogram tree. Default = 2"/>
59 <param argument="--sample_cluster_size" type="integer" label="For tabular output. Number of clusters 'k' to cut the sample dendrogram tree. Default = 2"/>
52 </xml> 60 </xml>
53 <xml name="pca_calcsep"> 61 <xml name="pca_calcsep">
54 <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false" 62 <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false"
55 label="Calculate separation between groups and include in title?"/> 63 label="Calculate separation between groups and include in title?"/>
56 </xml> 64 </xml>
67 </param> 75 </param>
68 </xml> 76 </xml>
69 </macros> 77 </macros>
70 <expand macro="requirements" /> 78 <expand macro="requirements" />
71 <command detect_errors="exit_code"><![CDATA[ 79 <command detect_errors="exit_code"><![CDATA[
80 cp '$infile' '$infile.name'
81 &&
72 metaquantome viz 82 metaquantome viz
73 --samps '$samps' 83 --samps '$samps'
74 --mode '$mode_args.mode' 84 --mode '$mode_args.mode'
75 #if str($mode_args.mode) == 'f' 85 #if str($mode_args.mode) == 'f'
76 --ontology='$mode_args.ontology' 86 --ontology='$mode_args.ontology'
77 #end if 87 #end if
78 --infile='$infile' 88 --infile='$infile.name'
79 --plottype='$mode_args.plot.plottype' 89 --plottype='$mode_args.plot.plottype'
80 #if $mode_args.plot.plottype == 'bar': 90 #if $mode_args.plot.plottype == 'bar':
81 #if str($mode_args.mode) == 't': 91 #if str($mode_args.mode) == 't':
82 --target_rank='$mode_args.plot.target_rank' 92 --target_rank='$mode_args.plot.target_rank'
83 #end if 93 #end if
91 --target_onto='$mode_args.plot.target_onto' 101 --target_onto='$mode_args.plot.target_onto'
92 #end if 102 #end if
93 --barcol=$mode_args.plot.barcol 103 --barcol=$mode_args.plot.barcol
94 #elif $mode_args.plot.plottype == 'volcano': 104 #elif $mode_args.plot.plottype == 'volcano':
95 --fc_name='$mode_args.plot.fc_name' 105 --fc_name='$mode_args.plot.fc_name'
106 --fc_corr_p='$mode_args.plot.fc_corr_p'
96 #if $mode_args.plot.textannot: 107 #if $mode_args.plot.textannot:
97 --textannot='$mode_args.plot.textannot' 108 --textannot='$mode_args.plot.textannot'
98 #end if 109 #end if
99 $mode_args.plot.flip_fc 110 $mode_args.plot.flip_fc
100 #if $mode_args.mode == 'f': 111 #if $mode_args.mode == 'f':
102 #end if 113 #end if
103 #elif $mode_args.plot.plottype == 'heatmap': 114 #elif $mode_args.plot.plottype == 'heatmap':
104 #if $mode_args.plot.heatmap.filter_to_sig: 115 #if $mode_args.plot.heatmap.filter_to_sig:
105 --filter_to_sig 116 --filter_to_sig
106 --alpha=$mode_args.plot.heatmap.alpha 117 --alpha=$mode_args.plot.heatmap.alpha
118 --fc_corr_p='mode_args.plot.fc_corr_p'
119 #end if
120 #if feature_cluster_size:
121 --feature_cluster_size='$mode_args.plot.feature_cluster_size'
122 #end if
123 #if sample_cluster_size:
124 --sample_cluster_size='$mode_args.plot.sample_cluster_size'
107 #end if 125 #end if
108 #elif $mode_args.plot.plottype == 'pca': 126 #elif $mode_args.plot.plottype == 'pca':
109 $mode_args.plot.calculate_sep 127 $mode_args.plot.calculate_sep
110 #elif $mode_args.plot.plottype == 'ft_dist': 128 #elif $mode_args.plot.plottype == 'ft_dist':
111 --barcol='$mode_args.plot.barcol' 129 --barcol='$mode_args.plot.barcol'
313 <data format="tabular" name="plotdata" 331 <data format="tabular" name="plotdata"
314 label="${tool.name} ${on_string} ${mode_args.plot.plottype}: plot data" 332 label="${tool.name} ${on_string} ${mode_args.plot.plottype}: plot data"
315 from_work_dir="plotdata.tab"> 333 from_work_dir="plotdata.tab">
316 <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter> 334 <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter>
317 </data> 335 </data>
336
337 <data format="tabular" name="heatmap_feature_cluster"
338 label="${mode_args.plot.plottype}: feature cluster data"
339 from_work_dir="feature_cluster_${infile.name.rsplit('.',1)[0]}.txt">
340 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
341 </data>
342 <data format="tabular" name="heatmap_sample_cluster"
343 label="${mode_args.plot.plottype}: sample cluster data"
344 from_work_dir="sample_cluster_${infile.name.rsplit('.',1)[0]}.txt">
345 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
346 </data>
347
348 <data format="tabular" name="heatmap_sample_cluster"
349 label="${mode_args.plot.plottype}: sample cluster data"
350 from_work_dir="PC_Data_${infile.name.rsplit('.',1)[0]}.txt">
351 <filter>mode_args['plot']['plottype'] in ["pca"]</filter>
352 </data>
353
318 </outputs> 354 </outputs>
319 <tests> 355 <tests>
320 <test> 356 <test>
321 <param name="infile" value="tax_filt_out.tab" ftype="tabular"/> 357 <param name="infile" value="tax_filt_out.tab" ftype="tabular"/>
322 <param name="mode" value="t" /> 358 <param name="mode" value="t" />
335 <param name="mode" value="t" /> 371 <param name="mode" value="t" />
336 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 372 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
337 <param name="plottype" value="volcano" /> 373 <param name="plottype" value="volcano" />
338 <param name="target_rank" value="genus" /> 374 <param name="target_rank" value="genus" />
339 <param name="fc_name" value="log2fc_NS_over_WS" /> 375 <param name="fc_name" value="log2fc_NS_over_WS" />
376 <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
340 <param name="textannot" value="taxon_name" /> 377 <param name="textannot" value="taxon_name" />
341 <output name="wrapped_outfile"> 378 <output name="wrapped_outfile">
342 <assert_contents> 379 <assert_contents>
343 <has_text text="To download the image" /> 380 <has_text text="To download the image" />
344 </assert_contents> 381 </assert_contents>
385 <param name="mode" value="f" /> 422 <param name="mode" value="f" />
386 <param name="ontology" value="go"/> 423 <param name="ontology" value="go"/>
387 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 424 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
388 <param name="plottype" value="volcano" /> 425 <param name="plottype" value="volcano" />
389 <param name="fc_name" value="log2fc_NS_over_WS" /> 426 <param name="fc_name" value="log2fc_NS_over_WS" />
427 <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
390 <output name="wrapped_outfile"> 428 <output name="wrapped_outfile">
391 <assert_contents> 429 <assert_contents>
392 <has_text text="To download the image" /> 430 <has_text text="To download the image" />
393 </assert_contents> 431 </assert_contents>
394 </output> 432 </output>