# HG changeset patch
# User iuc
# Date 1691490496 0
# Node ID baeee32175e835767c43a7feb145059c5cc46014

planemo upload for repository https://bedops.readthedocs.io/ commit e64b305e1ef7a6aa06a654f29701d7b43337c0ca

diff -r 000000000000 -r baeee32175e8 sort-bed.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sort-bed.xml	Tue Aug 08 10:28:16 2023 +0000
@@ -0,0 +1,66 @@
+<tool id="bedops-sort-bed" name="bedops sort-bed" version="@TOOL_VERSION@" profile="22.01">
+    <macros>
+        <token name="@TOOL_VERSION@">2.4.41</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">bedops</requirement>
+    </requirements>
+    <command><![CDATA[
+sort-bed 
+--max-mem "\${GALAXY_MEMORY_MB:-1024}M"
+--tmpdir "\${_GALAXY_JOB_TMP_DIR:-.}"
+$unique
+$duplicates
+#for file in $inputs:
+    '$file'
+#end for
+> '$output'
+    ]]></command>
+    <inputs>
+        <param name="inputs" type="data" format="bed" multiple="true"/>
+        <param argument="--unique" type="boolean" truevalue="--unique" falsevalue="" label="Output only unique elements?"/>
+        <param argument="--duplicates" type="boolean" truevalue="--duplicates" falsevalue="" label="Output only duplicate elements?"/>
+    </inputs>
+    <outputs>
+        <data name="output" format_source="inputs" label="$tool.name: sorted output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" value="unsorted.bed" ftype="bed"/>
+            <output name="output" value="sorted_simpled.bed"/>
+        </test>
+        <test>
+            <param name="inputs" value="unsorted.bed" ftype="bed"/>
+            <param name="unique" value="true"/>
+            <output name="output" value="sorted_unique.bed"/>
+        </test>
+        <test>
+            <param name="inputs" value="unsorted.bed" ftype="bed"/>
+            <param name="duplicates" value="true"/>
+            <output name="output" value="sorted_duplicates.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+What this tool does
+===================
+
+The sort-bed utility sorts BED files of any size, even larger than system memory. BED files that are in lexicographic-chromosome order allow BEDOPS utilities to work efficiently with data from any species without software modifications. Further, sorted files can be traversed very quickly.
+
+Sorted BED order is defined first by lexicographic chromosome order, then ascending integer start coordinate order, and finally by ascending integer end coordinate order. To make the sort order unambiguous, a lexicographical sort is applied on fourth and subsequent columns, where present in the input BED dataset.
+
+
+Input
+=====
+
+The sort-bed utility requires one or more three-column BED file(s). Support for common headers (such as UCSC BED track headers) is included, although headers will be stripped from the output.
+
+
+Output
+======
+
+Sort order is defined by a lexicographical sort on chromosome name, a numerical sort on start coordinates, a numerical sort on stop coordinates where there are start matches, and finally a lexicographical sort on the remainder of the BED element (if additional columns are present). Additional options may be specified to print only unique or duplicate elements.
+    ]]></help>
+    <citations>
+        <citation type="doi">https://doi.org/10.1093/bioinformatics/bts277</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r baeee32175e8 test-data/sorted_duplicates.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sorted_duplicates.bed	Tue Aug 08 10:28:16 2023 +0000
@@ -0,0 +1,1 @@
+dummy_chr	1	100	0	0	99	0.0000000
diff -r 000000000000 -r baeee32175e8 test-data/sorted_simpled.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sorted_simpled.bed	Tue Aug 08 10:28:16 2023 +0000
@@ -0,0 +1,4 @@
+dummy_chr	1	100	0	0	99	0.0000000
+dummy_chr	1	100	0	0	99	0.0000000
+dummy_chr	1000	1000000	2	152	999000	0.0001522
+super_dummy_chr	1	100	0	0	99	0.0000000
diff -r 000000000000 -r baeee32175e8 test-data/sorted_unique.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sorted_unique.bed	Tue Aug 08 10:28:16 2023 +0000
@@ -0,0 +1,3 @@
+dummy_chr	1	100	0	0	99	0.0000000
+dummy_chr	1000	1000000	2	152	999000	0.0001522
+super_dummy_chr	1	100	0	0	99	0.0000000
diff -r 000000000000 -r baeee32175e8 test-data/unsorted.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unsorted.bed	Tue Aug 08 10:28:16 2023 +0000
@@ -0,0 +1,4 @@
+dummy_chr	1	100	0	0	99	0.0000000
+dummy_chr	1000	1000000	2	152	999000	0.0001522
+dummy_chr	1	100	0	0	99	0.0000000
+super_dummy_chr	1	100	0	0	99	0.0000000