metaquantome_viz: metaquantome

comparison metaquantome_viz.xml @ 2:51bc1ccad6aa draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"

author	galaxyp
date	Tue, 24 Nov 2020 15:05:11 +0000
parents	1a402023bdec
children	5bbedd902998

comparison

equal deleted inserted replaced

-:1a402023bdec
+:51bc1ccad6aa
 </when>
 <when value="false">
 <!-- do nothing -->
 </when>
 </conditional>
-<param argument="--feature_cluster_size" type="integer" label="For tabular output. Number of clusters 'k' to cut the feature dendrogram tree. Default = 2"/>
+<param argument="--feature_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the feature dendrogram tree."/>
-<param argument="--sample_cluster_size" type="integer" label="For tabular output. Number of clusters 'k' to cut the sample dendrogram tree. Default = 2"/>
+<param argument="--sample_cluster_size"  value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the sample dendrogram tree."/>
 </xml>
 <xml name="pca_calcsep">
 <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false"
 label="Calculate separation between groups and include in title?"/>
 </xml>
 </param>
 </xml>
 </macros>
 <expand macro="requirements" />
 <command detect_errors="exit_code"><![CDATA[
-cp '$infile' '$infile.name'
+	#import re
+	#set $safename = re.sub('[^\w\-_\.]', '_', $infile.element_identifier)
+	ln -s '$infile' '$safename'
 &&
 metaquantome viz
 --samps '$samps'
 --mode '$mode_args.mode'
 #if str($mode_args.mode) == 'f'
 --ontology='$mode_args.ontology'
 #end if
---infile='$infile.name'
+--infile='$safename'
 --plottype='$mode_args.plot.plottype'
 #if $mode_args.plot.plottype == 'bar':
 #if str($mode_args.mode) == 't':
 --target_rank='$mode_args.plot.target_rank'
 #end if
 #if $mode_args.plot.heatmap.filter_to_sig:
 --filter_to_sig
 --alpha=$mode_args.plot.heatmap.alpha
 --fc_corr_p='mode_args.plot.fc_corr_p'
 #end if
-#if feature_cluster_size:
+#if $mode_args.plot.feature_cluster_size:
 --feature_cluster_size='$mode_args.plot.feature_cluster_size'
 #end if
-#if sample_cluster_size:
+#if $mode_args.plot.sample_cluster_size:
 --sample_cluster_size='$mode_args.plot.sample_cluster_size'
 #end if
 #elif $mode_args.plot.plottype == 'pca':
 $mode_args.plot.calculate_sep
 #elif $mode_args.plot.plottype == 'ft_dist':
 If text is cut off or the plot is not displaying properly,
 the easiest fix is to increase the plot dimensions
 </p>
 </body>
 </html>" > wrapped_outfile.html
+&& >&2 ls
+#if $mode_args.plot.plottype in ["heatmap"]
+&& mv 'feature_cluster_${safename}.txt' '$heatmap_feature_cluster'
+&& mv 'sample_cluster_${safename}.txt' '$heatmap_sample_cluster'
+#end if
+#if $mode_args.plot.plottype in ["pca"]
+&& mv 'PC_data_${safename}.txt' '$pca_sample_cluster'
+#end if
 ]]></command>
 <inputs>
 <param argument="--infile" type="data"
 format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/>
 <expand macro="SAMPS"/>
 <outputs>
 <data format="html" name="wrapped_outfile"
 label="${tool.name} on ${on_string} ${mode_args.plot.plottype}.html"
 from_work_dir="wrapped_outfile.html"/>
 <data format="tabular" name="plotdata"
-label="${tool.name} ${on_string} ${mode_args.plot.plottype}: plot data"
+label="${tool.name} on ${on_string} ${mode_args.plot.plottype}: plot data"
 from_work_dir="plotdata.tab">
 <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter>
 </data>
 <data format="tabular" name="heatmap_feature_cluster"
-label="${mode_args.plot.plottype}: feature cluster data"
+label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} feature cluster data">
-from_work_dir="feature_cluster_${infile.name.rsplit('.',1)[0]}.txt">
 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
 </data>
 <data format="tabular" name="heatmap_sample_cluster"
-label="${mode_args.plot.plottype}: sample cluster data"
+label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} sample cluster data">
-from_work_dir="sample_cluster_${infile.name.rsplit('.',1)[0]}.txt">
 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
 </data>
-<data format="tabular" name="heatmap_sample_cluster"
+<data format="tabular" name="pca_sample_cluster"
-label="${mode_args.plot.plottype}: sample cluster data"
+label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} sample cluster data">
-from_work_dir="PC_Data_${infile.name.rsplit('.',1)[0]}.txt">
 <filter>mode_args['plot']['plottype'] in ["pca"]</filter>
 </data>
 </outputs>
 <tests>
-<test>
+<test expect_num_outputs="2">
 <param name="infile" value="tax_filt_out.tab" ftype="tabular"/>
 <param name="mode" value="t" />
 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
 <param name="plottype" value="bar" />
 <param name="target_rank" value="genus" />
 <assert_contents>
 <has_text text="To download the image" />
 </assert_contents>
 </output>
 </test>
-<test>
+<test expect_num_outputs="2">
 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
 <param name="mode" value="t" />
 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
 <param name="plottype" value="volcano" />
 <param name="target_rank" value="genus" />
 <assert_contents>
 <has_text text="To download the image" />
 </assert_contents>
 </output>
 </test>
-<test>
+<test expect_num_outputs="3">
 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
 <param name="mode" value="t" />
 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
 <param name="plottype" value="heatmap" />
 <output name="wrapped_outfile">
 <assert_contents>
 <has_text text="To download the image" />
 </assert_contents>
 </output>
 </test>
-<test>
+<test expect_num_outputs="2">
 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
 <param name="mode" value="t" />
 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
 <param name="plottype" value="pca" />
 <output name="wrapped_outfile">
 <assert_contents>
 <has_text text="To download the image" />
 </assert_contents>
 </output>
 </test>
-<test>
+<test expect_num_outputs="2">
 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
 <param name="mode" value="f" />
 <param name="ontology" value="go" />
 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
 <param name="plottype" value="bar" />
 <assert_contents>
 <has_text text="To download the image" />
 </assert_contents>
 </output>
 </test>
-<test>
+<test expect_num_outputs="2">
 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
 <param name="mode" value="f" />
 <param name="ontology" value="go"/>
 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
 <param name="plottype" value="volcano" />
 <assert_contents>
 <has_text text="To download the image" />
 </assert_contents>
 </output>
 </test>
-<test>
+<test expect_num_outputs="1">
 <param name="infile" value="tf_filt_out.tab" ftype="tabular"/>
 <param name="mode" value="ft" />
 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
 <param name="plottype" value="ft_dist" />
 <param name="meancol" value="NS_mean" />

Mercurial > repos > galaxyp > metaquantome_viz

comparison metaquantome_viz.xml @ 2:51bc1ccad6aa draft