Mercurial > repos > iuc > query_tabular

changeset 8:0c95a3f1654f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 1647065a8e6e8d8c98cd0d2194b695fb9425f541"
author iuc
date Thu, 23 Jan 2020 07:36:39 -0500
parents 33d61c89fb8d
children a3aab6045663
files macros.xml query_tabular.xml test-data/psm_dbmod_output.tsv test-data/psm_dbmod_output1.tsv test-data/psm_report_out1.tsv test-data/psm_report_out2.tsv
diffstat 6 files changed, 36 insertions(+), 34 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Oct 30 20:19:30 2018 -0400
+++ b/macros.xml	Thu Jan 23 07:36:39 2020 -0500
@@ -72,6 +72,11 @@
     #end if
 ]]>
   </token>
+  <xml name="requirements">
+      <requirements>
+          <requirement type="package" version="3.7">python</requirement>
+      </requirements>
+  </xml>
   <xml name="comment_char_options">
         <option value="62">&gt;</option>
         <option value="64">@</option>
--- a/query_tabular.xml	Tue Oct 30 20:19:30 2018 -0400
+++ b/query_tabular.xml	Thu Jan 23 07:36:39 2020 -0500
@@ -1,13 +1,10 @@
-<tool id="query_tabular" name="Query Tabular" version="3.0.0">
+<tool id="query_tabular" name="Query Tabular" version="3.0.1">
     <description>using sqlite sql</description>
 
     <macros>
          <import>macros.xml</import>
     </macros>
-
-    <requirements>
-    </requirements>
-
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         cat '$query_file' &&
         #if $add_to_database.withdb: 
@@ -463,7 +460,7 @@
                 <param name="header" value="yes"/>
                 <param name="header_prefix" value=""/>
             </conditional>
-            <output name="output" file="psm_report_out1.tsv"/>
+            <output name="output" file="psm_report_out1.tsv" compare="re_match"/>
         </test>
 
         <test>
@@ -488,7 +485,7 @@
                 <param name="header" value="yes"/>
                 <param name="header_prefix" value=""/>
             </conditional>
-            <output name="output" file="psm_report_out2.tsv"/>
+            <output name="output" file="psm_report_out2.tsv" compare="re_match"/>
         </test>
 
         <test>
@@ -527,8 +524,8 @@
                     </conditional>
                 </repeat>
             </section>
-            <output name="output" file="psm_dbmod_output.tsv"/>
-            <output name="output1" file="psm_dbmod_output1.tsv"/>
+            <output name="output" file="psm_dbmod_output.tsv" compare="re_match"/>
+            <output name="output1" file="psm_dbmod_output1.tsv" compare="re_match"/>
         </test>
 
     </tests>
--- a/test-data/psm_dbmod_output.tsv	Tue Oct 30 20:19:30 2018 -0400
+++ b/test-data/psm_dbmod_output.tsv	Thu Jan 23 07:36:39 2020 -0500
@@ -1,5 +1,5 @@
-#scan	m/z	Precursor m/z Error	Sequence	Protein(s)	confidence
-1	523.272583	-4.42404529799	PYANQPTVR	NP_116558	99.999
-3	652.843567	4.02947892238	SSWAGLQFPVGR	NP_066544_R21W	99.999
-4	788.87384	1.27277118312	AQACNLDQSGTNVAK	NP_112092_rs7285167:R182C	99.999
-7	908.008545	0.740229025429	DMTVPVLVSKPPVFTGK	NP_001909_rs72973763:I239V,rs12021720:S384G	94.7368421053
+#scan	m\/z	Precursor m\/z Error	Sequence	Protein\(s\)	confidence
+1	523.27\d*	-4.42\d*	PYANQPTVR	NP_116558	99.9\d*
+3	652.84\d*	4.02\d*	SSWAGLQFPVGR	NP_066544_R21W	99.9\d*
+4	788.87\d*	1.27\d*	AQACNLDQSGTNVAK	NP_112092_rs7285167:R182C	99.9\d*
+7	908.00\d*	0.74\d*	DMTVPVLVSKPPVFTGK	NP_001909_rs72973763:I239V,rs12021720:S384G	94.73\d*
--- a/test-data/psm_dbmod_output1.tsv	Tue Oct 30 20:19:30 2018 -0400
+++ b/test-data/psm_dbmod_output1.tsv	Thu Jan 23 07:36:39 2020 -0500
@@ -1,6 +1,6 @@
-scan	Sequence	Protein(s)	Position	m/z	Precursor m/z Error	confidence
-1	PYANQPTVR	NP_116558	2	523.272583	-4.42404529799	99.999
-3	SSWAGLQFPVGR	NP_066544_R21W	19	652.843567	4.02947892238	99.999
-4	AQACNLDQSGTNVAK	NP_112092_rs7285167:R182C	179	788.87384	1.27277118312	99.999
-6	LQLLPESFICK	NP_001028196, NP_001244919, NP_036311	198; 163; 277	674.370911	0.341203679555	99.3865030675
-8	FGVSSESKPEEVK	NP_001265138, NP_001265138_rs2274136:A858T,F879L, NP_001265139, NP_001265139_rs2274136:A785T,F806L, NP_005115, NP_005115_rs2274136:A827T,F848L	992; 992; 919; 919; 961; 961	711.858643	-0.766605567436	99.999
+scan	Sequence	Protein\(s\)	Position	m\/z	Precursor m\/z Error	confidence
+1	PYANQPTVR	NP_116558	2	523.27\d*	-4.42\d*	99.99\d*
+3	SSWAGLQFPVGR	NP_066544_R21W	19	652.84\d*	4.02\d*	99.99\d*
+4	AQACNLDQSGTNVAK	NP_112092_rs7285167:R182C	179	788.87\d*	1.27\d*	99.99\d*
+6	LQLLPESFICK	NP_001028196, NP_001244919, NP_036311	198; 163; 277	674.37\d*	0.34\d*	99.38\d*
+8	FGVSSESKPEEVK	NP_001265138, NP_001265138_rs2274136:A858T,F879L, NP_001265139, NP_001265139_rs2274136:A785T,F806L, NP_005115, NP_005115_rs2274136:A827T,F848L	992; 992; 919; 919; 961; 961	711.85\d*	-0.76\d*	99.9\d*
--- a/test-data/psm_report_out1.tsv	Tue Oct 30 20:19:30 2018 -0400
+++ b/test-data/psm_report_out1.tsv	Thu Jan 23 07:36:39 2020 -0500
@@ -1,9 +1,9 @@
-Scan	Sequence	Protein(s)	Position	m/z	Precursor m/z Error
-1	PYANQPTVR	NP_116558	2	523.272583	-4.42404529799
-2	DANTQVHTLR	NP_443137, NP_443137_S1016F	443; 443	577.799622	0.611733835535
-3	SSWAGLQFPVGR	NP_066544_R21W	19	652.843567	4.02947892238
-4	AQACNLDQSGTNVAK	NP_112092_rs7285167:R182C	179	788.87384	1.27277118312
-5	ACNDPFIQK	NP_001273432_F75C, NP_001273433_F77C, NP_001273434_F77C, NP_006635_F75C	74; 76; 76; 74	546.760803	0.0670946694617
-6	LQLLPESFICK	NP_001028196, NP_001244919, NP_036311	198; 163; 277	674.370911	0.341203679555
-7	DMTVPVLVSKPPVFTGK	NP_001909_rs72973763:I239V,rs12021720:S384G	234	908.008545	0.740229025429
-8	FGVSSESKPEEVK	NP_001265138, NP_001265138_rs2274136:A858T,F879L, NP_001265139, NP_001265139_rs2274136:A785T,F806L, NP_005115, NP_005115_rs2274136:A827T,F848L	992; 992; 919; 919; 961; 961	711.858643	-0.766605567436
+Scan	Sequence	Protein\(s\)	Position	m\/z	Precursor m\/z Error
+1	PYANQPTVR	NP_116558	2	523.272583	-4.42\d*
+2	DANTQVHTLR	NP_443137, NP_443137_S1016F	443; 443	577.799622	0.61\d*
+3	SSWAGLQFPVGR	NP_066544_R21W	19	652.843567	4.02\d*
+4	AQACNLDQSGTNVAK	NP_112092_rs7285167:R182C	179	788.87384	1.27\d*
+5	ACNDPFIQK	NP_001273432_F75C, NP_001273433_F77C, NP_001273434_F77C, NP_006635_F75C	74; 76; 76; 74	546.760803	0.067\d*
+6	LQLLPESFICK	NP_001028196, NP_001244919, NP_036311	198; 163; 277	674.370911	0.34\d*
+7	DMTVPVLVSKPPVFTGK	NP_001909_rs72973763:I239V,rs12021720:S384G	234	908.008545	0.74\d*
+8	FGVSSESKPEEVK	NP_001265138, NP_001265138_rs2274136:A858T,F879L, NP_001265139, NP_001265139_rs2274136:A785T,F806L, NP_005115, NP_005115_rs2274136:A827T,F848L	992; 992; 919; 919; 961; 961	711.858643	-0.76\d*
--- a/test-data/psm_report_out2.tsv	Tue Oct 30 20:19:30 2018 -0400
+++ b/test-data/psm_report_out2.tsv	Thu Jan 23 07:36:39 2020 -0500
@@ -1,5 +1,5 @@
-Scan	m/z	Precursor m/z Error	Sequence	Protein(s)
-1	523.272583	-4.42404529799	PYANQPTVR	NP_116558
-3	652.843567	4.02947892238	SSWAGLQFPVGR	NP_066544_R21W
-4	788.87384	1.27277118312	AQACNLDQSGTNVAK	NP_112092_rs7285167:R182C
-7	908.008545	0.740229025429	DMTVPVLVSKPPVFTGK	NP_001909_rs72973763:I239V,rs12021720:S384G
+Scan	m\/z	Precursor m\/z Error	Sequence	Protein\(s\)
+1	523.27\d*	-4.42\d*	PYANQPTVR	NP_116558
+3	652.84\d*	4.02\d*	SSWAGLQFPVGR	NP_066544_R21W
+4	788.87\d*	1.27\d*	AQACNLDQSGTNVAK	NP_112092_rs7285167:R182C
+7	908.00\d*	0.74\d*	DMTVPVLVSKPPVFTGK	NP_001909_rs72973763:I239V,rs12021720:S384G