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Changeset 1:28d7819c312f (2020-01-19)

Previous changeset 0:1d835c691480 (2017-12-19) Next changeset 2:daf8518d243a (2024-09-27)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"

modified:
macros.xml
poretools_events.xml

removed:
test-data/poretools-events-out1.tabular
test-data/poretools-events-out2.tabular

diff -r 1d835c691480 -r 28d7819c312f macros.xml
--- a/macros.xml Tue Dec 19 14:45:24 2017 -0500
+++ b/macros.xml Sun Jan 19 09:10:59 2020 -0500

[

@@ -47,4 +47,6 @@
         <param name="min_length" argument="--min-length" type="integer" value="0" label="Minimum read length" />
         <param name="max_length" argument="--max-length" type="integer" value="1000000000" label="Maximum read length" />
     </xml>
+    <token name="@MPLBACKEND@"><![CDATA[export MPLBACKEND="agg" &&]]></token>
+    <token name="@profile@">18.09</token>
</macros>

diff -r 1d835c691480 -r 28d7819c312f poretools_events.xml
--- a/poretools_events.xml Tue Dec 19 14:45:24 2017 -0500
+++ b/poretools_events.xml Sun Jan 19 09:10:59 2020 -0500

@@ -1,5 +1,5 @@
<?xml version="1.0"?>
-<tool id="poretools_events" name="Extract nanopore events" version="@VERSION@.0">
+<tool id="poretools_events" name="Extract nanopore events" version="@VERSION@.1">
     <description>from a set of sequencing reads</description>
     <macros>
         <import>macros.xml</import>
@@ -12,7 +12,7 @@
     </command>
     <inputs>
         <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
-        <param name="precalled" argument="--pre-basecalled" type="boolean" truevalue="--pre-basecalled" falsevalue="--pre-basecalled" label="Report pre-basecalled events" />
+        <param name="precalled" argument="--pre-basecalled" type="boolean" truevalue="--pre-basecalled" falsevalue="" label="Report pre-basecalled events" />
     </inputs>
     <outputs>
         <data name="output" format="tabular" />
@@ -21,12 +21,26 @@
         <test>
             <expand macro="test_input" />
             <param name="precalled" value="false" />
-            <output name="output" file="poretools-events-out1.tabular" ftype="tabular" />
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="2901"/>
+                    <has_text text="template"/>
+                    <has_text text="complement"/>
+                    <not_has_text text="pre_basecalled"/>
+                </assert_contents>
+            </output>
         </test>
         <test>
             <expand macro="test_input" />
             <param name="precalled" value="true" />
-            <output name="output" file="poretools-events-out2.tabular" ftype="tabular" />
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="3083"/>
+                    <not_has_text text="template"/>
+                    <not_has_text text="complement"/>
+                    <has_text text="pre_basecalled"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>

diff -r 1d835c691480 -r 28d7819c312f test-data/poretools-events-out1.tabular
--- a/test-data/poretools-events-out1.tabular Tue Dec 19 14:45:24 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,3083 +0,0 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diff -r 1d835c691480 -r 28d7819c312f test-data/poretools-events-out2.tabular
--- a/test-data/poretools-events-out2.tabular Tue Dec 19 14:45:24 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000