--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/parse.xml	Tue Mar 26 12:49:21 2024 +0000
@@ -0,0 +1,127 @@
+<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="22.05" license="MIT">
+    <description>Find ligation pairs in alignments and create pairs.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        pairtools parse
+            '$sam_path'
+            -c '$chroms_path'
+            $assembly
+            -o '$output_parsed_pairs'
+            --min-mapq '$min_mapq'
+            --max-molecule-size '$max_molecule_size'
+            $drop_readid
+            $drop_seq
+            $output_stats
+            $drop_sam
+            #if $output_stats:
+                '$parsed_pairs_stats'
+            #end if
+            --walks-policy '$walks_policy'
+            --max-inter-align-gap '$max_inter_algn_gap'
+            --nproc-in \${GALAXY_SLOTS:-4}
+            --nproc-out \${GALAXY_SLOTS:-4}
+    ]]></command>
+    <inputs>
+        <param name="sam_path" type="data" format="sam,bam" label="Input SAM/BAM file" help="Input SAM or BAM file with paired-end sequence alignments of Hi-C molecules."/>    
+        <param name="chroms_path" argument="-c" type="data" format="tabular" label="Input a chromosome order file" help="Chromosome order used to flip interchromosomal mates. Any scaffolds not listed will be ordered lexicographically."/>
+        <param name="assembly" type="text" value="" label="Input a name of a genome assembly" help="Name of genome assembly (e.g. hg19, mm10) to store in the pairs header"></param>
+        <param argument="--min-mapq" type="integer" value="40" min="0" label="Minimal MAPQ" help="Minimal MAPQ score to consider a read as uniquely mapped."/>
+        <param argument="--max-molecule-size" type="integer" min="0" value="750" label="Input the maximal size of a Hi-C molecule" help="The maximal size of a Hi-C molecule; used to rescue single ligations(from molecules with three alignments) and to rescue complex ligations."></param>
+        <param argument="--drop-readid" type="boolean" truevalue="--drop-readid" falsevalue="" checked="False" label="Do not add read ids to the output"></param>
+        <param argument="--drop-seq" type="boolean" truevalue="--drop-seq" falsevalue="" checked="False" label="remove sequences and PHREDs from the sam fields"></param>
+        <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Do not add sams to the output"></param>
+        <param argument="--drop-sam" type="boolean" truevalue="--drop-sam" falsevalue="" checked="False" label="Generate various statistics of pairs file"></param>    
+        <param argument="--walks-policy" type="select" label="Walks Policy" help="The policy for reporting unrescuable walks.">
+            <expand macro="walks_policy_options"/>
+        </param>   
+        <param argument="max_inter_algn_gap" type="integer" min="0" value="30" label="Max alignment gap" help="read segments that are not covered by any alignment and longer than the specified value are treated as null alignments."/>
+    </inputs>
+    <outputs>
+        <data name="output_parsed_pairs" format="pairs" label="${tool.name} on ${on_string}: .pairs"/>
+        <data name="parsed_pairs_stats" format="txt,tabular" label="${tool.name} on ${on_string}: parsed.stats">
+            <filter>output_stats</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!--Test 01 with SAM file as input and default parameters-->
+        <test expect_num_outputs="1">
+            <param name="sam_path" value="test.sam"/>
+            <param name="chroms_path" value="test.genome"/>
+            <param name="min_mapq" value="1"/>
+            <param name="walks_policy" value="mask"/>
+            <param name="max_inter_algn_gap" value="20"/>
+            <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_sam.pairs" lines_diff="10"/>
+        </test>
+        <!--Test 02 with BAM file as input and default parameters-->
+        <test expect_num_outputs="1">
+            <param name="sam_path" value="test.bam"/>
+            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
+            <param name="min_mapq" value="1"/>
+            <param name="walks_policy" value="mask"/>
+            <param name="max_inter_algn_gap" value="20"/>
+            <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam.pairs" lines_diff="10"/>
+        </test>
+        <!--Test 03 with BAM file as input and minimal mapq of 40-->
+        <test expect_num_outputs="1">
+            <param name="sam_path" value="test.bam"/>
+            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
+            <param name="min_mapq" value="40"/>
+            <param name="walks_policy" value="mask"/>
+            <param name="max_inter_algn_gap" value="20"/>
+            <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam_min_mapq_40.pairs" lines_diff="10"/>
+        </test>
+        <!--Test 04 with BAM file as input and walk policy of 5unique-->
+        <test expect_num_outputs="1">
+            <param name="sam_path" value="test.bam"/>
+            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
+            <param name="min_mapq" value="40"/>
+            <param name="walks_policy" value="5unique"/>
+            <param name="max_inter_algn_gap" value="20"/>
+            <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam_5unique.pairs" lines_diff="10"/>
+        </test>
+        <!--Test 05 with BAM file as input and read id dropped-->
+        <test expect_num_outputs="1">
+            <param name="sam_path" value="test.bam"/>
+            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
+            <param name="min_mapq" value="40"/>
+            <param name="walks_policy" value="5unique"/>
+            <param name="max_inter_algn_gap" value="20"/>
+            <param name="drop_readid" value="true"></param>
+            <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam_readid_dropped.pairs" lines_diff="10"/>
+        </test>
+        <!--Test 06 with SAM file as input and drop_seq enabled-->
+        <test expect_num_outputs="1">
+            <param name="sam_path" value="test.sam"/>
+            <param name="chroms_path" value="test.genome"/>
+            <param name="min_mapq" value="40"/>
+            <param name="walks_policy" value="5unique"/>
+            <param name="max_inter_algn_gap" value="20"/>
+            <param name="drop_seq" value="true"></param>
+            <output name="output_parsed_pairs" ftype="pairs" file="output_parsed_pairs_bam_readid_dropped_seq.pairs" lines_diff="10"/>
+        </test>
+        <!--Test 07 with SAM file as input and output_stats enabled-->
+        <test expect_num_outputs="2">
+            <param name="sam_path" value="test.sam"/>
+            <param name="chroms_path" value="test.genome"/>
+            <param name="min_mapq" value="40"/>
+            <param name="walks_policy" value="5unique"/>
+            <param name="max_inter_algn_gap" value="20"/>
+            <param name="output_stats" value="true"></param>
+            <output name="parsed_pairs_stats" file="output_parsed_pairs.stats" lines_diff="10"/>
+        </test>
+
+    </tests>
+    <help><![CDATA[
+        **Pairtools parse**
+
+        Detects ligation events in the aligned sequences of DNA molecules formed in Hi-C experiments and reports them in the .pairs/.pairsam format.
+        
+        sam_path : an input .sam/.bam file with paired-end sequence alignments of Hi-C molecules. 
+              
+    ]]></help>
+    <expand macro="citations"/>
+    <expand macro="creator"/>
+</tool>