# HG changeset patch
# User iuc
# Date 1618656060 0
# Node ID 5bd67e012d547e1d527f925091395645c924d93b
# Parent  ee356d7a5518f80a75136ed96bcbbd5d63c0e8a8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 958bbd9e30ae4d320f872f1ab5e1bacfb28b1a00"

diff -r ee356d7a5518 -r 5bd67e012d54 bax2bam.xml
--- a/bax2bam.xml	Thu Nov 28 15:49:50 2019 -0500
+++ b/bax2bam.xml	Sat Apr 17 10:41:00 2021 +0000
@@ -1,94 +1,133 @@
 <?xml version="1.0"?>
-<tool id="bax2bam" name="bax2bam" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
+<tool id="bax2bam" name="bax2bam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>converts PacBio basecall format (bax.h5) into BAM</description>
     <macros>
-        <import>macros.xml</import>
+        <token name="@TOOL_VERSION@">0.0.11</token>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
-    <expand macro="requirements"/>
-    <stdio></stdio>
+    <edam_topics>
+        <edam_topic>topic_3168</edam_topic> <!-- Topic - Laboratory techniques - Sequencing -->
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_3434</edam_operation> <!-- Operation - Conversion -->
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">bax2bam</requirement>
+    </requirements>
+    <version_command><![CDATA[bax2bam --version]]></version_command>
     <command detect_errors="exit_code"><![CDATA[
-        bax2bam
-            #for $file in $files
-                '$file'
-            #end for
-            -o output
-            $readtype
-            #if $pulsefeatures
-                --pulsefeatures=$pulsefeatures
-            #end if
-            $losslessframes
-            $internal
+## skipped -h/--help, --xml, -f, --output-xml, --ccs (see https://github.com/PacificBiosciences/pbbioconda/issues/215)
+
+## run
+bax2bam
+#for $file in $files
+    '$file'
+#end for
+-o 'output'
+$readtype
+#if $pulsefeatures
+    --pulsefeatures=$pulsefeatures
+#end if
+$losslessframes
+$internal
     ]]></command>
     <inputs>
-        <param name="files" type="data" format="h5" multiple="true" label="Files" help="Should be from the same movie."/>
-        <param name="readtype" type="select" label="Output read type" help="">
-            <option value="--subread">subread</option>
-            <option value="--hqregion">hqregion</option>
-            <option value="--polymeraseread">polymeraseread</option>
+        <param name="files" type="data" format="h5" multiple="true" label="Select files" help="Should be from the same movie."/>
+        <param name="readtype" type="select" label="Select output read type">
+            <option value="--hqregion">Hqregion</option>
+            <option value="--polymeraseread">Polymeraseread</option>
+            <option value="--subread">Subread</option>
         </param>
-        <param argument="--pulsefeatures" type="select" multiple="true" label="Select pulse features in the output BAM." help="">
+        <param argument="--pulsefeatures" type="select" multiple="true" label="Select pulse features in output BAM">
             <option value="DeletionQV" selected="true">dq - DeletionQV</option>
             <option value="DeletionTag" selected="true">dt - DeletionTag</option>
             <option value="InsertionQV" selected="true">iq - InsertionQV</option>
             <option value="IPD" selected="true">ip - IPD</option>
+            <option value="MergeQV" selected="true">mq - MergeQV</option>
             <option value="PulseWidth" selected="true">pw - PulseWidth</option>
-            <option value="MergeQV" selected="true">mq - MergeQV</option>
             <option value="SubstitutionQV" selected="true">sq - SubstitutionQV</option>
             <option value="SubstitutionTag" selected="false">st - SubstitutionTag</option>
         </param>
-        <param argument="--losslessframes" type="boolean" truevalue="--losslessframes" falsevalue="" checked="false" label="Store full, 16-bit IPD/PulseWidth data" help="Instead of (default) downsampled, 8-bit encoding."/>
-        <param argument="--internal" type="boolean" truevalue="--internal" falsevalue="" checked="false" label="Output BAMs in internal mode." help="Currently this indicates that non-sequencing ZMWs should be included in the output scraps BAM file, if applicable."/>
+        <param argument="--losslessframes" type="boolean" truevalue="--losslessframes" falsevalue="" label="Store full, 16-bit IPD/PulseWidth data?" help="Instead of downsampled, 8-bit encoding."/>
+        <param argument="--internal" type="boolean" truevalue="--internal" falsevalue="" checked="false" label="Output BAMs in internal mode?" help="Currently this indicates that non-sequencing ZMWs should be included in the output scraps BAM file, if applicable."/>
     </inputs>
-
     <outputs>
-        <data name="output_scrap" from_work_dir="output.scraps.bam" format="bam" label="${tool.name} on ${on_string}: scraps">
+        <data name="output_scrap" from_work_dir="output.scraps.bam" format="bam" label="${tool.name} on ${on_string}: Scraps">
             <filter>readtype == '--subread'</filter>
         </data>
-        <data name="output_subread" from_work_dir="output.subreads.bam" format="bam" label="${tool.name} on ${on_string}: subreads">
+        <data name="output_subread" from_work_dir="output.subreads.bam" format="bam" label="${tool.name} on ${on_string}: Subreads">
             <filter>readtype == '--subread'</filter>
         </data>
-        <data name="output_hqregion" from_work_dir="output.hqregions.bam" format="bam" label="${tool.name} on ${on_string}: hqregions">
+        <data name="output_hqregion" from_work_dir="output.hqregions.bam" format="bam" label="${tool.name} on ${on_string}: Hqregions">
             <filter>readtype == '--hqregion'</filter>
         </data>
-        <data name="output_lqregion" from_work_dir="output.lqregions.bam" format="bam" label="${tool.name} on ${on_string}: lqregions">
+        <data name="output_lqregion" from_work_dir="output.lqregions.bam" format="bam" label="${tool.name} on ${on_string}: Lqregions">
             <filter>readtype == '--hqregion'</filter>
         </data>
-        <data name="output_polymeraseread" from_work_dir="output.polymerase.bam" format="bam" label="${tool.name} on ${on_string}: polymerase">
+        <data name="output_polymeraseread" from_work_dir="output.polymerase.bam" format="bam" label="${tool.name} on ${on_string}: Polymerase">
             <filter>readtype == '--polymeraseread'</filter>
         </data>
     </outputs>
-        
     <tests>
-        <!-- source of test data: https://github.com/PacificBiosciences/PacBioTestData/tree/master/data/HdfSubreadSet/Analysis_Results/ -->
-        <!-- #1: read type: subread -->
-        <test>
+        <!-- test data source https://github.com/PacificBiosciences/PacBioTestData/tree/master/data/HdfSubreadSet/Analysis_Results/ -->
+
+        <!-- #1 subread, default -->
+        <test expect_num_outputs="2">
             <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>
             <param name="readtype" value="--subread"/>
-            <output name="output_scrap" file="scraps.bam" compare="sim_size" delta="100"/>
-            <output name="output_subread" file="subreads.bam" compare="sim_size" delta="100"/>
+            <output name="output_scrap">
+                <assert_contents>
+                    <has_size value="113578" delta="100"/>
+                </assert_contents>
+            </output>
+            <output name="output_subread">
+                <assert_contents>
+                    <has_size value="242552" delta="100"/>
+                </assert_contents>
+            </output>
         </test>
-        <!-- #2: read type: hqregion -->
-        <test>
+        <!-- #2 hqregion, default -->
+        <test expect_num_outputs="2">
             <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>
             <param name="readtype" value="--hqregion"/>
-            <output name="output_hqregion" file="hqregions.bam" compare="sim_size" delta="100"/>
-            <output name="output_hqregion" file="lqregions.bam" compare="sim_size" delta="100"/>
+            <output name="output_hqregion">
+                <assert_contents>
+                    <has_size value="232342" delta="100"/>
+                </assert_contents>
+            </output>
+            <output name="output_hqregion">
+                <assert_contents>
+                    <has_size value="232342" delta="100"/>
+                </assert_contents>
+            </output>
         </test>
-        <!-- #3: read type: polymeraseread -->
-        <test>
+        <!-- #3 polymeraseread, default -->
+        <test expect_num_outputs="1">
             <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>
             <param name="readtype" value="--polymeraseread"/>
-            <output name="output_polymeraseread" file="polymerase.bam" compare="sim_size" delta="100"/>
+            <output name="output_polymeraseread">
+                <assert_contents>
+                    <has_size value="333195" delta="100"/>
+                </assert_contents>
+            </output>
         </test>
-        <!-- #4: read type: subread, custom parameters -->
-        <test>
+        <!-- #4 subread, custom -->
+        <test expect_num_outputs="2">
             <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>
             <param name="readtype" value="--subread"/>
             <param name="pulsefeatures" value="SubstitutionTag"/>
             <param name="losslessframes" value="true"/>
             <param name="internal" value="true"/>
-            <output name="output_scrap" file="scraps_custom.bam" compare="sim_size" delta="100"/>
-            <output name="output_subread" file="subreads_custom.bam" compare="sim_size" delta="100"/>
+            <output name="output_scrap">
+                <assert_contents>
+                    <has_size value="23497" delta="100"/>
+                </assert_contents>
+            </output>
+            <output name="output_subread">
+                <assert_contents>
+                    <has_size value="45147" delta="100"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
@@ -101,17 +140,17 @@
 
 **Input**
 
-bax.h5 files that should be from the same movie.
+- Sample files that should be from the same movie (bax.h5)
 
 **Output**
 
-A single BAM file. 
+- Converted sample (BAM) 
 
 .. class:: infomark
 
 **References**
 
- More information can be found on the github repositories `bax2bam <https://github.com/pacificbiosciences/bax2bam/>`_ and `PacBio Bioconda <https://github.com/PacificBiosciences/pbbioconda>`_.
+ More information can be found on the GitHub repositories `bax2bam <https://github.com/pacificbiosciences/bax2bam/>`_ and `PacBio Bioconda <https://github.com/PacificBiosciences/pbbioconda>`_.
     ]]></help>
     <citations>
         <citation type="bibtex">
@@ -125,4 +164,4 @@
 }
         </citation>
     </citations>
-</tool>
+</tool>
\ No newline at end of file
diff -r ee356d7a5518 -r 5bd67e012d54 macros.xml
--- a/macros.xml	Thu Nov 28 15:49:50 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<macros>
-    <token name="@TOOL_VERSION@">0.0.9</token> 
-
-    <token name="@WRAPPER_VERSION@">galaxy0</token> 
-
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="@TOOL_VERSION@">bax2bam</requirement>
-            <yield/>
-        </requirements>
-    </xml>
-</macros>
\ No newline at end of file
diff -r ee356d7a5518 -r 5bd67e012d54 test-data/hqregions.bam
Binary file test-data/hqregions.bam has changed
diff -r ee356d7a5518 -r 5bd67e012d54 test-data/lqregions.bam
Binary file test-data/lqregions.bam has changed
diff -r ee356d7a5518 -r 5bd67e012d54 test-data/polymerase.bam
Binary file test-data/polymerase.bam has changed
diff -r ee356d7a5518 -r 5bd67e012d54 test-data/scraps.bam
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diff -r ee356d7a5518 -r 5bd67e012d54 test-data/scraps_custom.bam
Binary file test-data/scraps_custom.bam has changed
diff -r ee356d7a5518 -r 5bd67e012d54 test-data/subreads.bam
Binary file test-data/subreads.bam has changed
diff -r ee356d7a5518 -r 5bd67e012d54 test-data/subreads_custom.bam
Binary file test-data/subreads_custom.bam has changed