# HG changeset patch
# User galaxyp
# Date 1544104219 18000
# Node ID 28180bbb8fe454efe85fdaee089656b64e9bde61
# Parent  a8cb3dea93a622da2a0e9565eefe598239dd772f
planemo upload commit 3762c462ff510cccd856f4ccd7fb87c44ad9b4e7

diff -r a8cb3dea93a6 -r 28180bbb8fe4 metaquantome_filter.xml
--- a/metaquantome_filter.xml	Wed Dec 05 14:52:54 2018 -0500
+++ b/metaquantome_filter.xml	Thu Dec 06 08:50:19 2018 -0500
@@ -76,6 +76,28 @@
         <data format="tabular" name="outfile" label="${tool.name} on ${on_string} filtered"/>
         <expand macro="output_samples"/>
     </outputs>
+    <tests>
+        <test>
+             <param name="expand_file" value="go_expanded.tab" ftype="tabular"/>
+             <param name="mode" value="f" />
+             <param name="ontology" value="go" />
+             <param name="samps_src" value="build" />
+             <repeat name="samps">
+                 <param name="group_name" value="s1"/>
+                 <param name="col_names" value="int1,int2,int3"/>
+             </repeat>
+             <repeat name="samps">
+                 <param name="group_name" value="s2"/>
+                 <param name="col_names" value="int4,int5,int6"/>
+             </repeat>
+             <param name="min_peptides" value="1" />
+             <param name="min_pep_nsamp" value="1" />
+             <param name="min_children_non_leaf" value="2" />
+             <param name="min_child_nsamp" value="1" />
+             <param name="qthreshold" value="2" />
+             <output name="outfile" file="go_filtered.tab" ftype="tabular"/>
+        </test>
+    </tests>
     <help><![CDATA[
         TODO: Fill in help.
     ]]></help>
diff -r a8cb3dea93a6 -r 28180bbb8fe4 metaquantome_viz.xml
--- a/metaquantome_viz.xml	Wed Dec 05 14:52:54 2018 -0500
+++ b/metaquantome_viz.xml	Thu Dec 06 08:50:19 2018 -0500
@@ -99,7 +99,7 @@
                     help=""/>
         <conditional name="plot">
             <param argument="--plottype" type="select" label="Plot type">
-                <option value="bar">Bar Charti (bar)</option>
+                <option value="bar">Bar Chart (bar)</option>
                 <option value="volcano">Volcano Plot (volcano)</option>
                 <option value="heatmap">Heatmap (heatmap)</option>
                 <option value="pca">Principal Componets Analysis (pca)</option>
@@ -173,6 +173,22 @@
     <outputs>
         <data format="png" name="outfile" label="${tool.name} on ${on_string} ${plot.plottype}" from_work_dir="outfile.png"/>
     </outputs>
+    <tests>
+        <test>
+             <param name="infile" value="tax_filt.tab" ftype="tabular"/>
+             <param name="mode" value="t" />
+             <param name="samps_src" value="history" />
+             <param name="samps_file" value="samples.tab" ftype="tabular"/>
+             <param name="plottype" value="bar" />
+             <param name="target_rank" value="genus" />
+             <param name="meancol" value="NS_mean" />
+             <param name="nterms" value="3" />
+             <param name="barcol" value="1" />
+             <param name="width" value="3" />
+             <param name="height" value="3" />
+             <output name="outfile" file="tax_ns.png" ftype="png" compare="sim_size" delta="50000"/>
+        </test>
+    </tests>
     <help><![CDATA[
         TODO: Fill in help.
     ]]></help>
diff -r a8cb3dea93a6 -r 28180bbb8fe4 test-data/go_filtered.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/go_filtered.tab	Thu Dec 06 08:50:19 2018 -0500
@@ -0,0 +1,2 @@
+id	name	namespace	s1_mean	s2_mean	int1	int2	int3	int4	int5	int6	int1_n_peptide	int2_n_peptide	int3_n_peptide	int4_n_peptide	int5_n_peptide	int6_n_peptide	int1_n_samp_children	int2_n_samp_children	int3_n_samp_children	int4_n_samp_children	int5_n_samp_children	int6_n_samp_children
+GO:0008150	biological_process	biological_process	10.066537719931583	11.4814630999144	10.011227255423254	10.287712379549447	9.868822554774999	11.782998208920414	10.9901039638575	11.560332834212444	3.0	3.0	3.0	3.0	3.0	3.0	3.0	3.0	3.0	3.0	3.0	3.0
diff -r a8cb3dea93a6 -r 28180bbb8fe4 test-data/samples.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples.tab	Thu Dec 06 08:50:19 2018 -0500
@@ -0,0 +1,3 @@
+group	colnames
+NS	X737NS,X852NS,X867NS
+WS	X737WS,X852WS,X867WS
\ No newline at end of file
diff -r a8cb3dea93a6 -r 28180bbb8fe4 test-data/tax_filt.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tax_filt.tab	Thu Dec 06 08:50:19 2018 -0500
@@ -0,0 +1,15 @@
+id	taxon_name	rank	NS_mean	WS_mean	X737NS	X737WS	X852NS	X852WS	X867NS	X867WS	X737NS_n_peptide	X737WS_n_peptide	X852NS_n_peptide	X852WS_n_peptide	X867NS_n_peptide	X867WS_n_peptide	X737NS_n_samp_children	X737WS_n_samp_children	X852NS_n_samp_children	X852WS_n_samp_children	X867NS_n_samp_children	X867WS_n_samp_children
+712	Pasteurellaceae	family	26.45508515455985	24.240760984631766	24.965005542520593	22.218244926365948	0.0	17.341365183225566	27.1723016809798	25.697827115441516	12.0	12.0	0.0	1.0	12.0	12.0	1.0	1.0	0.0	0.0	1.0	1.0
+724	Haemophilus	genus	26.043545589333238	24.308669239875652	23.49238493402781	21.57274687722112	0.0	0.0	26.91490217583963	25.19610989120677	5.0	5.0	0.0	0.0	5.0	5.0	1.0	1.0	0.0	0.0	1.0	1.0
+729	Haemophilus parainfluenzae	species	23.516051135977808	21.837453207025035	22.113077280032016	20.132830444840515	0.0	0.0	24.21369255243491	22.597204359627263	4.0	4.0	0.0	0.0	4.0	4.0	0.0	0.0	0.0	0.0	0.0	0.0
+1224	Proteobacteria	phylum	26.506407720117732	26.405669726384243	25.647561843048845	25.684049762573892	25.572526514273356	26.02079872568725	27.451384780869606	27.10853680624065	18.0	18.0	3.0	4.0	17.0	17.0	2.0	2.0	2.0	2.0	2.0	2.0
+1239	Firmicutes	phylum	28.512385596646148	30.091433318476454	28.16821189186139	29.85860894014845	28.689295147943678	29.902989443795985	28.625794429436656	30.43794314029389	247.0	362.0	325.0	366.0	317.0	354.0	3.0	2.0	3.0	3.0	3.0	2.0
+1301	Streptococcus	genus	26.867617254051414	28.85011386863358	26.46624241376839	28.05891048314316	26.560458646377878	29.13539355848514	27.388297546047863	29.117339967272912	67.0	124.0	96.0	127.0	111.0	124.0	2.0	3.0	3.0	3.0	2.0	3.0
+1302	Streptococcus gordonii	species	24.686370636745576	27.653507330007766	23.762400434698712	26.151624056996113	24.539475551766014	27.515752990669643	25.336906564014722	28.450914623490767	24.0	43.0	29.0	44.0	44.0	45.0	0.0	0.0	0.0	0.0	0.0	0.0
+28216	Betaproteobacteria	class	23.29428542923752	24.791799066973446	22.374889513201293	21.402137416070087	24.544202571791207	23.84100698984557	19.8675358581728	26.047141520330538	2.0	2.0	2.0	2.0	1.0	1.0	2.0	2.0	2.0	2.0	1.0	1.0
+29465	Veillonella	genus	27.14677305830786	28.768830375331426	27.034861383116564	28.980840680293607	27.47904567128595	27.71387087737904	26.85278433596802	29.212848758443123	134.0	167.0	149.0	156.0	126.0	156.0	3.0	2.0	3.0	2.0	2.0	3.0
+29466	Veillonella parvula	species	18.832221452467913	23.646622731934286	18.99584905472981	22.846993959159153	18.647632848343047	21.527044665274683	0.0	24.781099201499504	3.0	4.0	2.0	4.0	0.0	4.0	0.0	0.0	0.0	0.0	0.0	0.0
+39778	Veillonella dispar	species	20.06805764601431	21.234364824902784	18.873358040924337	21.41636590750601	18.430484676034965	0.0	21.232667529959397	21.02604333055197	4.0	4.0	1.0	0.0	4.0	4.0	0.0	0.0	0.0	0.0	0.0	0.0
+40674	Mammalia	class	18.71423436046836	17.946348342079197	17.822232855425355	17.738850060395933	18.41771660331577	18.769965187049696	19.43400368663769	16.48885357307721	1.0	1.0	2.0	2.0	2.0	1.0	0.0	0.0	1.0	1.0	1.0	1.0
+46124	Granulicatella adiacens	species	25.44795951209062	24.095117178766355	22.413021529130273	23.066852858599482	26.121087214932714	23.994120320785946	25.808003124552783	24.75258507306872	12.0	25.0	31.0	31.0	33.0	29.0	0.0	0.0	0.0	0.0	0.0	0.0
+186826	Lactobacillales	order	27.515198585571607	29.11785831796523	26.715706855135487	28.32187712752904	27.586822118206747	29.36333727974101	27.974157758353318	29.426524865028252	92.0	171.0	151.0	183.0	167.0	176.0	2.0	3.0	3.0	3.0	2.0	3.0
diff -r a8cb3dea93a6 -r 28180bbb8fe4 test-data/tax_ns.png
Binary file test-data/tax_ns.png has changed