Mercurial > repos > galaxyp > metaquantome_viz
comparison metaquantome_viz.xml @ 1:8c30496a665a draft
"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 |
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| 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> |