diff dedup.xml @ 0:f8c1d2a93d43 draft

planemo upload for repository https://github.com/open2c/pairtools commit e9ebcf7ac032fafaa445e654b245df679a4bbf18

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dedup.xml	Thu Apr 04 19:40:59 2024 +0000
@@ -0,0 +1,67 @@
+<tool id="pairtools_dedup" name="Pairtools dedup" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
+    <description>Find and remove PCR/optical duplicates</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        pairtools dedup
+            '$pairs_path'
+            -o '$output_dedup_pairs'
+            #if $output_dups:
+                --output-dups '$output_dups_pairs'
+            #end if
+            $mark_dups
+            #if $output_stats:
+                  --output-stats '$dedup_pairs_stats'
+            #end if
+            --nproc-in \${GALAXY_SLOTS:-4}
+            --nproc-out \${GALAXY_SLOTS:-4}
+    ]]></command>
+    <inputs>      
+        <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input pairs file" help="Input triu-flipped sorted .pairs or .pairsam file"/>
+        <param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="False" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/>
+        <param argument="--output-dups" type="boolean" truevalue="--output-dups" falsevalue="" checked="False" label="Output file for duplicate pairs"/>
+        <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/>
+    </inputs>
+    <outputs>
+        <data name="output_dedup_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Deduplicated Pairs"/>
+        <data name="output_dups_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Duplicate Pairs">
+            <filter>output_dups</filter>
+        </data>
+        <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats">
+            <filter>output_stats</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!--Test 01 with default parameters-->
+        <test expect_num_outputs="1">
+            <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
+            <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" lines_diff="20"/>
+        </test>
+        <!--Test 02 mark_dups enabled and output_dups-->
+        <test expect_num_outputs="2">
+            <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
+            <param name="mark_dups" value="true"></param>
+            <param name="output_dups" value="true"></param>
+            <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/>
+            <output name="output_dups_pairs"  file="output_dups_pairs_markdups.pairsam" lines_diff="20"/>
+        </test>
+        <!--Test 03 mark_dups and output_stats enabled-->
+        <test expect_num_outputs="2">
+            <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
+            <param name="mark_dups" value="true"></param>
+            <param name="output_stats" value="true"></param>
+            <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/>
+            <output name="dedup_pairs_stats"  file="output_dedup_pairs.stats" lines_diff="20"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        **Pairtools dedup**
+
+        Find PCR/optical duplicates in an upper-triangular flipped sorted pairs/pairsam file. Allow for a +/-N bp mismatch at each side of duplicated molecules.
+              
+    ]]></help>
+    <expand macro="citations"/>
+    <expand macro="creator"/>
+</tool>