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Changeset 8:0c95a3f1654f (2020-01-23)

Previous changeset 7:33d61c89fb8d (2018-10-30) Next changeset 9:a3aab6045663 (2020-09-12)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 1647065a8e6e8d8c98cd0d2194b695fb9425f541"

modified:
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

diff -r 33d61c89fb8d -r 0c95a3f1654f macros.xml
--- 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">></option>
         <option value="64">@</option>

diff -r 33d61c89fb8d -r 0c95a3f1654f query_tabular.xml
--- 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>

diff -r 33d61c89fb8d -r 0c95a3f1654f test-data/psm_dbmod_output.tsv
--- 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*

diff -r 33d61c89fb8d -r 0c95a3f1654f test-data/psm_dbmod_output1.tsv
--- 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*

diff -r 33d61c89fb8d -r 0c95a3f1654f test-data/psm_report_out1.tsv
--- 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*

diff -r 33d61c89fb8d -r 0c95a3f1654f test-data/psm_report_out2.tsv
--- 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