Mercurial > repos > galaxyp > metaquantome_stat

changeset 1:982a442a98dd 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 17:02:11 +0000
parents 020a9ecdc1e1
children da986f83631b
files macros.xml metaquantome_stat.xml test-data/ec_ttest_tested.tab test-data/func_full_test_out.tab test-data/tax_test_out.tab
diffstat 5 files changed, 10 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Apr 25 13:50:59 2019 -0400
+++ b/macros.xml	Wed Sep 23 17:02:11 2020 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@VERSION@">1.0.0</token>
-    <token name="@GVERSION@">1.0.0-0</token>
+    <token name="@VERSION@">2.0.0</token>
+    <token name="@GVERSION@">2.0.0-0</token>
     <xml name="requirements">
         <requirements>
           <requirement type="package" version="@VERSION@">metaquantome</requirement>
--- a/metaquantome_stat.xml	Thu Apr 25 13:50:59 2019 -0400
+++ b/metaquantome_stat.xml	Wed Sep 23 17:02:11 2020 +0000
@@ -12,6 +12,7 @@
             --ontology='$mode_args.ontology_args.ontology'
         #end if
         --file '$file'
+        --control_group '$control_group'
         --parametric '$parametric'
         $paired
         --outfile='$outfile'
@@ -35,6 +36,9 @@
                 <expand macro="ONTOLOGY_ARGS"/>
             </when>
         </conditional>
+        <param argument="--control_group" type="text" label="Name of the control sample group of control (used as denominator for fold change evaluation).">
+            <validator type="empty_field"/>
+        </param>
         <param argument="--parametric" type="select" label="Statistical test to perform">
             <option value="False" selected="true">Wilcoxon test (nonparametric)</option>
             <option value="True">standard t-test (parametric)</option>
@@ -51,6 +55,7 @@
         <param name="ontology" value="ec" />
         <param name="mode" value="f" />
         <param name="samps" value="samples_basic.tab" ftype="tabular" />
+        <param name="control_group" value="s2"/>
         <output name="outfile" value="ec_ttest_tested.tab" ftype="tabular"/>
       </test>
     </tests>
--- a/test-data/ec_ttest_tested.tab	Thu Apr 25 13:50:59 2019 -0400
+++ b/test-data/ec_ttest_tested.tab	Wed Sep 23 17:02:11 2020 +0000
@@ -1,4 +1,4 @@
-id	description	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	log2fc_s1_over_s2	p	corrected_p
+id	description	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	log2fc_s1_over_s2	p_s1_over_s2	corrected_p_s1_over_s2
 1.-.-.-	Oxidoreductases.	10.013089999440444	3.5443205162238103	9.965784284662089	10.228818690495881	9.813781191217037	3.584962500721156	3.700439718141092	3.3219280948873617	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	1.0	6.468769483216634	2.70286875006428e-06	9.46004062522498e-06
 1.2.-.-	Acting on the aldehyde or oxo group of donors.	10.013089999440444	3.5443205162238103	9.965784284662089	10.228818690495881	9.813781191217037	3.584962500721156	3.700439718141092	3.3219280948873617	1.0	1.0	1.0	1.0	1.0	1.0	NA	NA	NA	NA	NA	NA	6.468769483216634	2.70286875006428e-06	9.46004062522498e-06
 3.-.-.-	Hydrolases.	5.28540221886225	11.475564566327488	5.0	5.6438561897747235	5.1292830169449655	11.778077129535358	10.980853606379736	11.555547771647065	2.0	2.0	2.0	2.0	2.0	2.0	1.0	1.0	1.0	1.0	1.0	1.0	-6.190162347465239	4.742887028677606e-05	5.533368200123874e-05
--- a/test-data/func_full_test_out.tab	Thu Apr 25 13:50:59 2019 -0400
+++ b/test-data/func_full_test_out.tab	Wed Sep 23 17:02:11 2020 +0000
@@ -1,4 +1,4 @@
-id	name	namespace	NS_mean	WS_mean	X730NS	X730WS	X733NS	X733WS	X734NS	X734WS	X737NS	X737WS	X760NS	X760WS	X769NS	X769WS	X781NS	X781WS	X795NS	X795WS	X852NS	X852WS	X861NS	X861WS	X866NS	X866WS	X867NS	X867WS	X730NS_n_peptide	X730WS_n_peptide	X733NS_n_peptide	X733WS_n_peptide	X734NS_n_peptide	X734WS_n_peptide	X737NS_n_peptide	X737WS_n_peptide	X760NS_n_peptide	X760WS_n_peptide	X769NS_n_peptide	X769WS_n_peptide	X781NS_n_peptide	X781WS_n_peptide	X795NS_n_peptide	X795WS_n_peptide	X852NS_n_peptide	X852WS_n_peptide	X861NS_n_peptide	X861WS_n_peptide	X866NS_n_peptide	X866WS_n_peptide	X867NS_n_peptide	X867WS_n_peptide	X730NS_n_samp_children	X730WS_n_samp_children	X733NS_n_samp_children	X733WS_n_samp_children	X734NS_n_samp_children	X734WS_n_samp_children	X737NS_n_samp_children	X737WS_n_samp_children	X760NS_n_samp_children	X760WS_n_samp_children	X769NS_n_samp_children	X769WS_n_samp_children	X781NS_n_samp_children	X781WS_n_samp_children	X795NS_n_samp_children	X795WS_n_samp_children	X852NS_n_samp_children	X852WS_n_samp_children	X861NS_n_samp_children	X861WS_n_samp_children	X866NS_n_samp_children	X866WS_n_samp_children	X867NS_n_samp_children	X867WS_n_samp_children	log2fc_NS_over_WS	p	corrected_p
+id	name	namespace	NS_mean	WS_mean	X730NS	X730WS	X733NS	X733WS	X734NS	X734WS	X737NS	X737WS	X760NS	X760WS	X769NS	X769WS	X781NS	X781WS	X795NS	X795WS	X852NS	X852WS	X861NS	X861WS	X866NS	X866WS	X867NS	X867WS	X730NS_n_peptide	X730WS_n_peptide	X733NS_n_peptide	X733WS_n_peptide	X734NS_n_peptide	X734WS_n_peptide	X737NS_n_peptide	X737WS_n_peptide	X760NS_n_peptide	X760WS_n_peptide	X769NS_n_peptide	X769WS_n_peptide	X781NS_n_peptide	X781WS_n_peptide	X795NS_n_peptide	X795WS_n_peptide	X852NS_n_peptide	X852WS_n_peptide	X861NS_n_peptide	X861WS_n_peptide	X866NS_n_peptide	X866WS_n_peptide	X867NS_n_peptide	X867WS_n_peptide	X730NS_n_samp_children	X730WS_n_samp_children	X733NS_n_samp_children	X733WS_n_samp_children	X734NS_n_samp_children	X734WS_n_samp_children	X737NS_n_samp_children	X737WS_n_samp_children	X760NS_n_samp_children	X760WS_n_samp_children	X769NS_n_samp_children	X769WS_n_samp_children	X781NS_n_samp_children	X781WS_n_samp_children	X795NS_n_samp_children	X795WS_n_samp_children	X852NS_n_samp_children	X852WS_n_samp_children	X861NS_n_samp_children	X861WS_n_samp_children	X866NS_n_samp_children	X866WS_n_samp_children	X867NS_n_samp_children	X867WS_n_samp_children	log2fc_NS_over_WS	p_NS_over_WS	corrected_p_NS_over_WS
 GO:0000015	phosphopyruvate hydratase complex	cellular_component	25.886058501686048	27.75998767351391	26.063085341729952	26.75868414835451	26.872321573535828	27.714535507520914	25.66138683343686	26.91922948200433	24.56792307320876	27.02361179346473	26.027647781700306	28.016086841596714	26.02628222102915	27.691319718917903	26.16224176931668	28.14922479286621	25.58935659144236	28.605803973702113	24.96556438729523	27.182932679501942	26.61887047167179	28.06289719214795	23.98035185379387	28.471187733625282	25.803186314724893	26.966628159317192	9.0	12.0	9.0	21.0	7.0	12.0	12.0	15.0	9.0	16.0	6.0	10.0	20.0	15.0	12.0	16.0	9.0	13.0	9.0	19.0	13.0	12.0	11.0	16.0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	-1.8739291718278608	4.146041132679973e-05	0.0005099643033035255
 GO:0000027	ribosomal large subunit assembly	biological_process	24.93071577771554	25.59199706393845	24.79502406577661	24.90569362782595	24.98653026336489	25.54103884489353	23.235856648559913	25.931788552669854	25.039623407494012	25.45976392090486	24.544491045410794	25.52182426968223	25.141851834365106	25.289466690231773	25.900937208609022	25.935471942444728	24.03595672520859	26.011397107654144	24.664753825097794	25.84980444944989	24.843398416694487	25.350436246047447	25.80464628461343	25.501822202499124	24.28178647007801	25.41548110918182	14.0	6.0	12.0	32.0	12.0	12.0	20.0	11.0	24.0	15.0	21.0	13.0	25.0	15.0	17.0	16.0	26.0	17.0	19.0	11.0	26.0	12.0	15.0	15.0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	-0.6612812862229092	0.00268017172806849	0.006910856026093958
 GO:0000036	acyl carrier activity	molecular_function	25.95712476206603	26.279571177686467	26.5301700656991	25.713248274935196	23.51705029509677	23.162225189828625	25.71677865632887	27.34753252356737	24.76249594346933	27.104656358315633	25.695589715923877	27.215607058954525	25.964407715885855	25.376217309281692	24.710785124891835	24.76949157731373	26.583389308611466	26.855652944530483	27.299615071207107	26.21417524637679	25.987672484095224	25.62275900338784	25.498246974021807	25.479528439599648	25.891370301559785	26.106957744939113	8.0	5.0	4.0	6.0	9.0	8.0	9.0	6.0	7.0	8.0	8.0	5.0	5.0	5.0	11.0	6.0	9.0	8.0	8.0	7.0	9.0	6.0	8.0	10.0	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	-0.32244641562043697	0.6033317722918665	0.6716842567531217
--- a/test-data/tax_test_out.tab	Thu Apr 25 13:50:59 2019 -0400
+++ b/test-data/tax_test_out.tab	Wed Sep 23 17:02:11 2020 +0000
@@ -1,4 +1,4 @@
-id	taxon_name	rank	NS_mean	WS_mean	X730NS	X730WS	X733NS	X733WS	X734NS	X734WS	X737NS	X737WS	X760NS	X760WS	X769NS	X769WS	X781NS	X781WS	X795NS	X795WS	X852NS	X852WS	X861NS	X861WS	X866NS	X866WS	X867NS	X867WS	X730NS_n_peptide	X730WS_n_peptide	X733NS_n_peptide	X733WS_n_peptide	X734NS_n_peptide	X734WS_n_peptide	X737NS_n_peptide	X737WS_n_peptide	X760NS_n_peptide	X760WS_n_peptide	X769NS_n_peptide	X769WS_n_peptide	X781NS_n_peptide	X781WS_n_peptide	X795NS_n_peptide	X795WS_n_peptide	X852NS_n_peptide	X852WS_n_peptide	X861NS_n_peptide	X861WS_n_peptide	X866NS_n_peptide	X866WS_n_peptide	X867NS_n_peptide	X867WS_n_peptide	X730NS_n_samp_children	X730WS_n_samp_children	X733NS_n_samp_children	X733WS_n_samp_children	X734NS_n_samp_children	X734WS_n_samp_children	X737NS_n_samp_children	X737WS_n_samp_children	X760NS_n_samp_children	X760WS_n_samp_children	X769NS_n_samp_children	X769WS_n_samp_children	X781NS_n_samp_children	X781WS_n_samp_children	X795NS_n_samp_children	X795WS_n_samp_children	X852NS_n_samp_children	X852WS_n_samp_children	X861NS_n_samp_children	X861WS_n_samp_children	X866NS_n_samp_children	X866WS_n_samp_children	X867NS_n_samp_children	X867WS_n_samp_children	log2fc_NS_over_WS	p	corrected_p
+id	taxon_name	rank	NS_mean	WS_mean	X730NS	X730WS	X733NS	X733WS	X734NS	X734WS	X737NS	X737WS	X760NS	X760WS	X769NS	X769WS	X781NS	X781WS	X795NS	X795WS	X852NS	X852WS	X861NS	X861WS	X866NS	X866WS	X867NS	X867WS	X730NS_n_peptide	X730WS_n_peptide	X733NS_n_peptide	X733WS_n_peptide	X734NS_n_peptide	X734WS_n_peptide	X737NS_n_peptide	X737WS_n_peptide	X760NS_n_peptide	X760WS_n_peptide	X769NS_n_peptide	X769WS_n_peptide	X781NS_n_peptide	X781WS_n_peptide	X795NS_n_peptide	X795WS_n_peptide	X852NS_n_peptide	X852WS_n_peptide	X861NS_n_peptide	X861WS_n_peptide	X866NS_n_peptide	X866WS_n_peptide	X867NS_n_peptide	X867WS_n_peptide	X730NS_n_samp_children	X730WS_n_samp_children	X733NS_n_samp_children	X733WS_n_samp_children	X734NS_n_samp_children	X734WS_n_samp_children	X737NS_n_samp_children	X737WS_n_samp_children	X760NS_n_samp_children	X760WS_n_samp_children	X769NS_n_samp_children	X769WS_n_samp_children	X781NS_n_samp_children	X781WS_n_samp_children	X795NS_n_samp_children	X795WS_n_samp_children	X852NS_n_samp_children	X852WS_n_samp_children	X861NS_n_samp_children	X861WS_n_samp_children	X866NS_n_samp_children	X866WS_n_samp_children	X867NS_n_samp_children	X867WS_n_samp_children	log2fc_NS_over_WS	p_NS_over_WS	corrected_p_NS_over_WS
 157	Treponema	genus	22.4592368471399	23.25164166545661	21.782210465654984	22.29366320170161	19.506474847066862	18.393389679254238	21.31060467932299	21.728055628093554	20.480986062363687	22.602867980613627	23.203993721974225	23.566696765176243	22.313857374707805	25.335612959036755	24.564206593926965	23.758132985051397	21.865153582932077	21.378622826723475	22.004619704258204	23.01330290131711	21.929889350172612	22.77047366650371	22.145836211855425	22.482730706742693	22.080359413733433	23.436551973678235	9.0	3.0	2.0	2.0	6.0	11.0	8.0	10.0	10.0	10.0	7.0	5.0	15.0	9.0	4.0	6.0	8.0	13.0	12.0	6.0	5.0	5.0	14.0	8.0	5.0	2.0	2.0	1.0	4.0	6.0	4.0	4.0	5.0	5.0	4.0	2.0	4.0	3.0	3.0	1.0	4.0	3.0	5.0	3.0	3.0	2.0	6.0	4.0	-0.7924048183167116	0.10596880912720232	0.22157114635687755
 194	Campylobacter	genus	22.737726781977898	23.402014527754694	19.374983778535537	20.606446832930114	22.374052312423657	22.175914745445667	20.710711088017703	21.497720060388442	21.935778024142905	21.360868814816588	19.67510328882646	18.442382745355207	21.21818802567592	18.98249372666148	25.95861986611441	24.365465047288765	19.540072068600086	22.271211580494718	17.998259192791753	26.353858284366478	18.911902395646823	20.233239126385538	19.83361162568149	19.261402979800614	20.129527247691183	22.479579021998745	3.0	5.0	2.0	5.0	2.0	7.0	25.0	5.0	7.0	4.0	17.0	3.0	209.0	8.0	4.0	9.0	4.0	8.0	3.0	5.0	7.0	4.0	7.0	6.0	2.0	2.0	2.0	3.0	2.0	4.0	2.0	3.0	2.0	2.0	3.0	2.0	4.0	4.0	2.0	3.0	2.0	4.0	2.0	3.0	2.0	2.0	2.0	4.0	-0.6642877457767966	0.27265646879500405	0.41807325215233954
 286	Pseudomonas	genus	22.84530963528067	20.941262344966106	19.390653532195216	21.257892314732068	23.40900039680405	21.249447306145736	22.85533086446144	17.189270329854693	21.43373289557238	18.940290665716926	21.2755581152792	21.78465732920301	19.42254043551283	17.888724701002317	22.016714341281943	20.86953224363516	18.685241717022148	22.54333528743205	20.234005329853034	18.807506861121887	23.765290496984004	16.805950901945454	25.39397860675149	22.523625447598253	19.404033335324762	14.425011898222733	2.0	4.0	2.0	7.0	11.0	3.0	4.0	6.0	7.0	4.0	4.0	2.0	16.0	8.0	2.0	7.0	5.0	5.0	6.0	3.0	6.0	4.0	5.0	1.0	1.0	1.0	1.0	2.0	3.0	NA	2.0	2.0	2.0	2.0	2.0	NA	3.0	3.0	2.0	3.0	3.0	1.0	2.0	NA	3.0	NA	2.0	1.0	1.9040472903145655	0.06467168750236378	0.15657355921624916