Mercurial > repos > iuc > mothur_chimera_vsearch

changeset 7:de3cfb122105 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author iuc
date Fri, 22 Jan 2021 01:09:52 +0000
parents 12e856482d26
children
files chimera.vsearch.xml test-data/chimera.count_table_wogroups test-data/chimera.vsearch.accnos test-data/chimera.vsearch.chimeras_wogroups
diffstat 4 files changed, 273 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/chimera.vsearch.xml	Tue Dec 08 14:17:28 2020 +0000
+++ b/chimera.vsearch.xml	Fri Jan 22 01:09:52 2021 +0000
@@ -1,4 +1,4 @@
-<tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.1">
+<tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.2">
     <description>find potential chimeric sequences using vsearch</description>
     <macros>
         <import>macros.xml</import>
@@ -101,11 +101,11 @@
         <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: vsearch.chimeras"/>
         <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: vsearch.accnos"/>
         <data name="out_count" format="mothur.count_table" from_work_dir="template.*vsearch.pick.count_table" label="${tool.name} on ${on_string}: vsearch.count_table">
-            <filter>template['source'] == 'self' and template['count']</filter>
+            <filter>template['source'] == 'self' and template['count'] and template['count'].metadata.groups != []</filter>
         </data>
     </outputs>
     <tests>
-        <test><!-- de novo test with name file -->
+        <test expect_num_outputs="3"><!-- de novo test with name file -->
             <param name="fasta" value="stool_small.unique.fasta"/>
             <param name="source" value="names"/>
             <param name="name" value="stool_small.names"/>
@@ -114,18 +114,29 @@
             <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
-        <test><!-- de novo test with count table-->
+        <test expect_num_outputs="4"><!-- de novo test with count table-->
             <param name="fasta" value="chimera.fasta"/>
             <param name="source" value="self"/>
-            <param name="count" value="chimera.count_table"/>
+            <param name="count" value="chimera.count_table" ftype="mothur.count_table"/>
             <param name="dereplicate" value="true"/>
             <output name="vsearch.chimeras" file="chimera.vsearch.chimeras" ftype="txt"/>
-            <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos"/>
+            <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos" sort="true"/>
             <output name="out_count" file="chimera.vsearch.count_table" ftype="mothur.count_table"/>
             <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
-        <test><!-- test with reference file -->
+        <test expect_num_outputs="3"><!-- de novo test with count table (missing group info)-->
+            <param name="fasta" value="chimera.fasta"/>
+            <param name="source" value="self"/>
+            <param name="count" value="chimera.count_table_wogroups" ftype="mothur.count_table"/>
+            <param name="dereplicate" value="true"/>
+            <!-- for some reason only for count tables wo group info header is printed -->
+            <output name="vsearch.chimeras" file="chimera.vsearch.chimeras_wogroups" ftype="txt"/>
+            <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos" sort="true"/>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test expect_num_outputs="3"><!-- test with reference file -->
             <param name="fasta" value="stool_small.unique.fasta"/>
             <param name="source" value="hist"/>
             <param name="reference" value="stool_small.unique.fasta"/>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chimera.count_table_wogroups	Fri Jan 22 01:09:52 2021 +0000
@@ -0,0 +1,122 @@
+Representative_Sequence	total
+M00967_43_000000000-A3JHG_1_1101_14069_1827	1
+M00967_43_000000000-A3JHG_1_1101_17674_2779	1
+M00967_43_000000000-A3JHG_1_1101_9376_4054	1
+M00967_43_000000000-A3JHG_1_1101_16910_7379	2
+M00967_43_000000000-A3JHG_1_1101_24218_7727	1
+M00967_43_000000000-A3JHG_1_1101_26181_9437	1
+M00967_43_000000000-A3JHG_1_1101_28516_16324	1
+M00967_43_000000000-A3JHG_1_1101_17802_26911	1
+M00967_43_000000000-A3JHG_1_1102_20832_5250	113
+M00967_43_000000000-A3JHG_1_1106_24475_12056	1
+M00967_43_000000000-A3JHG_1_1106_25798_21572	170
+M00967_43_000000000-A3JHG_1_1111_22890_9747	2
+M00967_43_000000000-A3JHG_1_2103_24027_17117	1
+M00967_43_000000000-A3JHG_1_2113_21352_15666	1
+M00967_43_000000000-A3JHG_1_2113_28097_13665	1
+M00967_43_000000000-A3JHG_1_1106_14252_8640	273
+M00967_43_000000000-A3JHG_1_1106_9147_22015	173
+M00967_43_000000000-A3JHG_1_1110_27249_9297	99
+M00967_43_000000000-A3JHG_1_2101_20023_3542	1
+M00967_43_000000000-A3JHG_1_2103_19057_10430	548
+M00967_43_000000000-A3JHG_1_2108_22020_21434	341
+M00967_43_000000000-A3JHG_1_2109_20085_20830	275
+M00967_43_000000000-A3JHG_1_2109_24829_22616	287
+M00967_43_000000000-A3JHG_1_1113_29188_13629	199
+M00967_43_000000000-A3JHG_1_2113_21823_22689	369
+M00967_43_000000000-A3JHG_1_1101_19936_3208	170
+M00967_43_000000000-A3JHG_1_1101_13293_4703	89
+M00967_43_000000000-A3JHG_1_1101_9121_7358	241
+M00967_43_000000000-A3JHG_1_1101_20566_7622	317
+M00967_43_000000000-A3JHG_1_1101_18269_8162	2
+M00967_43_000000000-A3JHG_1_1101_19986_8261	3
+M00967_43_000000000-A3JHG_1_1101_22097_8638	130
+M00967_43_000000000-A3JHG_1_1101_17781_8827	1
+M00967_43_000000000-A3JHG_1_1101_10877_9025	2
+M00967_43_000000000-A3JHG_1_1101_8083_11382	1
+M00967_43_000000000-A3JHG_1_1101_22600_11606	18
+M00967_43_000000000-A3JHG_1_1101_18457_12122	141
+M00967_43_000000000-A3JHG_1_1101_2601_14288	1
+M00967_43_000000000-A3JHG_1_1101_20136_15321	1
+M00967_43_000000000-A3JHG_1_1101_22252_18361	45
+M00967_43_000000000-A3JHG_1_1102_22032_8906	1
+M00967_43_000000000-A3JHG_1_1102_28309_11693	1
+M00967_43_000000000-A3JHG_1_1102_11996_19459	1
+M00967_43_000000000-A3JHG_1_1103_18439_9570	1
+M00967_43_000000000-A3JHG_1_1103_17703_17444	2
+M00967_43_000000000-A3JHG_1_1103_15262_26591	2
+M00967_43_000000000-A3JHG_1_1104_11653_4504	2
+M00967_43_000000000-A3JHG_1_1104_14862_19649	1
+M00967_43_000000000-A3JHG_1_1104_10368_19796	2
+M00967_43_000000000-A3JHG_1_1104_23658_26022	1
+M00967_43_000000000-A3JHG_1_1105_6783_9901	1
+M00967_43_000000000-A3JHG_1_1105_15970_15381	1
+M00967_43_000000000-A3JHG_1_1105_16780_22313	1
+M00967_43_000000000-A3JHG_1_1105_12173_24328	1
+M00967_43_000000000-A3JHG_1_1106_8935_10829	1
+M00967_43_000000000-A3JHG_1_1106_22147_11545	1
+M00967_43_000000000-A3JHG_1_1107_22653_9906	2
+M00967_43_000000000-A3JHG_1_1107_8955_12308	2
+M00967_43_000000000-A3JHG_1_1107_8466_14296	1
+M00967_43_000000000-A3JHG_1_1107_11945_14699	2
+M00967_43_000000000-A3JHG_1_1107_21101_17742	1
+M00967_43_000000000-A3JHG_1_1108_27204_7885	2
+M00967_43_000000000-A3JHG_1_1108_13143_12552	1
+M00967_43_000000000-A3JHG_1_1108_7852_15587	1
+M00967_43_000000000-A3JHG_1_1108_23614_18589	1
+M00967_43_000000000-A3JHG_1_1108_15093_19715	1
+M00967_43_000000000-A3JHG_1_1109_4809_15779	1
+M00967_43_000000000-A3JHG_1_1110_23880_14461	1
+M00967_43_000000000-A3JHG_1_1110_24675_19216	1
+M00967_43_000000000-A3JHG_1_1110_15840_20779	3
+M00967_43_000000000-A3JHG_1_1111_25634_11162	1
+M00967_43_000000000-A3JHG_1_1111_19100_13750	1
+M00967_43_000000000-A3JHG_1_1111_27151_20578	1
+M00967_43_000000000-A3JHG_1_1112_24767_9928	1
+M00967_43_000000000-A3JHG_1_1112_23422_10614	1
+M00967_43_000000000-A3JHG_1_1112_26117_11713	1
+M00967_43_000000000-A3JHG_1_1112_4337_15429	1
+M00967_43_000000000-A3JHG_1_1112_21728_27092	1
+M00967_43_000000000-A3JHG_1_1113_16694_13754	1
+M00967_43_000000000-A3JHG_1_1113_20871_14344	1
+M00967_43_000000000-A3JHG_1_1113_12471_18816	1
+M00967_43_000000000-A3JHG_1_1113_16327_24237	1
+M00967_43_000000000-A3JHG_1_1113_14854_24384	1
+M00967_43_000000000-A3JHG_1_1114_7252_4589	1
+M00967_43_000000000-A3JHG_1_1114_8032_8820	1
+M00967_43_000000000-A3JHG_1_1114_16548_11767	2
+M00967_43_000000000-A3JHG_1_1114_29150_14733	1
+M00967_43_000000000-A3JHG_1_1114_10899_22898	1
+M00967_43_000000000-A3JHG_1_2101_18965_1898	1
+M00967_43_000000000-A3JHG_1_2101_16550_11883	2
+M00967_43_000000000-A3JHG_1_2101_13178_13004	1
+M00967_43_000000000-A3JHG_1_2102_6993_12259	1
+M00967_43_000000000-A3JHG_1_2102_12688_15786	1
+M00967_43_000000000-A3JHG_1_2102_16641_21046	1
+M00967_43_000000000-A3JHG_1_2104_22466_3574	1
+M00967_43_000000000-A3JHG_1_2104_15266_7083	1
+M00967_43_000000000-A3JHG_1_2104_23877_11861	1
+M00967_43_000000000-A3JHG_1_2104_10795_17906	1
+M00967_43_000000000-A3JHG_1_2104_14517_21920	1
+M00967_43_000000000-A3JHG_1_2105_10923_10313	3
+M00967_43_000000000-A3JHG_1_2105_21664_11149	1
+M00967_43_000000000-A3JHG_1_2106_12463_10694	1
+M00967_43_000000000-A3JHG_1_2106_7204_11261	1
+M00967_43_000000000-A3JHG_1_2106_26330_20483	2
+M00967_43_000000000-A3JHG_1_2107_13907_8387	1
+M00967_43_000000000-A3JHG_1_2107_20590_19864	2
+M00967_43_000000000-A3JHG_1_2107_9082_21015	1
+M00967_43_000000000-A3JHG_1_2108_5348_13505	1
+M00967_43_000000000-A3JHG_1_2108_17630_23878	1
+M00967_43_000000000-A3JHG_1_2109_10754_15445	1
+M00967_43_000000000-A3JHG_1_2110_7072_11039	1
+M00967_43_000000000-A3JHG_1_2110_9144_17633	1
+M00967_43_000000000-A3JHG_1_2111_5896_17127	1
+M00967_43_000000000-A3JHG_1_2111_12311_21336	1
+M00967_43_000000000-A3JHG_1_2112_14825_10079	1
+M00967_43_000000000-A3JHG_1_2112_19406_24178	1
+M00967_43_000000000-A3JHG_1_2113_11985_5871	1
+M00967_43_000000000-A3JHG_1_2114_23175_9025	1
+M00967_43_000000000-A3JHG_1_2114_22955_20188	1
+M00967_43_000000000-A3JHG_1_2114_27743_21641	2
+M00967_43_000000000-A3JHG_1_2114_20166_26072	2
--- a/test-data/chimera.vsearch.accnos	Tue Dec 08 14:17:28 2020 +0000
+++ b/test-data/chimera.vsearch.accnos	Fri Jan 22 01:09:52 2021 +0000
@@ -1,26 +1,31 @@
+M00967_43_000000000-A3JHG_1_1101_19986_8261
+M00967_43_000000000-A3JHG_1_1110_15840_20779
+M00967_43_000000000-A3JHG_1_2105_10923_10313
 M00967_43_000000000-A3JHG_1_1101_18269_8162
-M00967_43_000000000-A3JHG_1_1101_19986_8261
+M00967_43_000000000-A3JHG_1_1104_11653_4504
+M00967_43_000000000-A3JHG_1_1107_11945_14699
+M00967_43_000000000-A3JHG_1_1107_22653_9906
+M00967_43_000000000-A3JHG_1_1107_8955_12308
+M00967_43_000000000-A3JHG_1_1114_16548_11767
+M00967_43_000000000-A3JHG_1_2101_16550_11883
+M00967_43_000000000-A3JHG_1_2107_20590_19864
+M00967_43_000000000-A3JHG_1_2114_20166_26072
 M00967_43_000000000-A3JHG_1_1101_20136_15321
 M00967_43_000000000-A3JHG_1_1101_2601_14288
 M00967_43_000000000-A3JHG_1_1101_8083_11382
 M00967_43_000000000-A3JHG_1_1102_11996_19459
 M00967_43_000000000-A3JHG_1_1102_28309_11693
 M00967_43_000000000-A3JHG_1_1103_18439_9570
-M00967_43_000000000-A3JHG_1_1104_11653_4504
 M00967_43_000000000-A3JHG_1_1104_23658_26022
 M00967_43_000000000-A3JHG_1_1105_15970_15381
 M00967_43_000000000-A3JHG_1_1105_16780_22313
 M00967_43_000000000-A3JHG_1_1105_6783_9901
 M00967_43_000000000-A3JHG_1_1106_8935_10829
-M00967_43_000000000-A3JHG_1_1107_11945_14699
 M00967_43_000000000-A3JHG_1_1107_21101_17742
-M00967_43_000000000-A3JHG_1_1107_22653_9906
 M00967_43_000000000-A3JHG_1_1107_8466_14296
-M00967_43_000000000-A3JHG_1_1107_8955_12308
 M00967_43_000000000-A3JHG_1_1108_13143_12552
 M00967_43_000000000-A3JHG_1_1108_23614_18589
 M00967_43_000000000-A3JHG_1_1109_4809_15779
-M00967_43_000000000-A3JHG_1_1110_15840_20779
 M00967_43_000000000-A3JHG_1_1110_23880_14461
 M00967_43_000000000-A3JHG_1_1110_24675_19216
 M00967_43_000000000-A3JHG_1_1111_19100_13750
@@ -31,22 +36,18 @@
 M00967_43_000000000-A3JHG_1_1113_12471_18816
 M00967_43_000000000-A3JHG_1_1113_14854_24384
 M00967_43_000000000-A3JHG_1_1113_20871_14344
-M00967_43_000000000-A3JHG_1_1114_16548_11767
 M00967_43_000000000-A3JHG_1_1114_7252_4589
 M00967_43_000000000-A3JHG_1_1114_8032_8820
 M00967_43_000000000-A3JHG_1_2101_13178_13004
-M00967_43_000000000-A3JHG_1_2101_16550_11883
 M00967_43_000000000-A3JHG_1_2101_18965_1898
 M00967_43_000000000-A3JHG_1_2102_12688_15786
 M00967_43_000000000-A3JHG_1_2102_6993_12259
 M00967_43_000000000-A3JHG_1_2104_15266_7083
 M00967_43_000000000-A3JHG_1_2104_22466_3574
 M00967_43_000000000-A3JHG_1_2104_23877_11861
-M00967_43_000000000-A3JHG_1_2105_10923_10313
 M00967_43_000000000-A3JHG_1_2105_21664_11149
 M00967_43_000000000-A3JHG_1_2106_12463_10694
 M00967_43_000000000-A3JHG_1_2106_7204_11261
-M00967_43_000000000-A3JHG_1_2107_20590_19864
 M00967_43_000000000-A3JHG_1_2107_9082_21015
 M00967_43_000000000-A3JHG_1_2108_17630_23878
 M00967_43_000000000-A3JHG_1_2108_5348_13505
@@ -58,6 +59,5 @@
 M00967_43_000000000-A3JHG_1_2112_19406_24178
 M00967_43_000000000-A3JHG_1_2113_11985_5871
 M00967_43_000000000-A3JHG_1_2113_28097_13665
-M00967_43_000000000-A3JHG_1_2114_20166_26072
 M00967_43_000000000-A3JHG_1_2114_22955_20188
 M00967_43_000000000-A3JHG_1_2114_23175_9025
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chimera.vsearch.chimeras_wogroups	Fri Jan 22 01:09:52 2021 +0000
@@ -0,0 +1,122 @@
+Score	Query	ParentA	ParentB	IdQM	IdQA	IdQB	IdAB	IdQT	LY	LN	LA	RY	RN	RA	Div	YN
+0.0000	M00967_43_000000000-A3JHG_1_2103_19057_10430;size=548;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	M00967_43_000000000-A3JHG_1_2113_21823_22689;size=369;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	M00967_43_000000000-A3JHG_1_2108_22020_21434;size=341;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	M00967_43_000000000-A3JHG_1_1101_20566_7622;size=317;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	M00967_43_000000000-A3JHG_1_2109_24829_22616;size=287;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	M00967_43_000000000-A3JHG_1_2109_20085_20830;size=275;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	M00967_43_000000000-A3JHG_1_1106_14252_8640;size=273;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	M00967_43_000000000-A3JHG_1_1101_9121_7358;size=241;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	M00967_43_000000000-A3JHG_1_1113_29188_13629;size=199;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0156	M00967_43_000000000-A3JHG_1_1106_9147_22015;size=173;	M00967_43_000000000-A3JHG_1_2103_19057_10430;size=548;	M00967_43_000000000-A3JHG_1_2108_22020_21434;size=341;	M00967_43_000000000-A3JHG_1_2108_22020_21434;size=341;	87.2	86.0	86.8	96.0	86.8	4	3	28	3	0	1	0.4	N
+0.0000	M00967_43_000000000-A3JHG_1_1101_19936_3208;size=170;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	M00967_43_000000000-A3JHG_1_1106_25798_21572;size=170;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
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+0.0482	M00967_43_000000000-A3JHG_1_1101_22097_8638;size=130;	M00967_43_000000000-A3JHG_1_2113_21823_22689;size=369;	M00967_43_000000000-A3JHG_1_2108_22020_21434;size=341;	M00967_43_000000000-A3JHG_1_2113_21823_22689;size=369;	86.2	83.4	80.2	77.1	83.4	26	11	12	12	5	7	2.8	N
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