--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pretext_map.xml	Wed May 05 15:09:54 2021 +0000
@@ -0,0 +1,132 @@
+<tool id="pretext_map" name="PretextMap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <macros>
+        <token name="@TOOL_VERSION@">0.1.5</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">pretextmap</requirement>
+        <requirement type="package" version="1.12">samtools</requirement>
+    </requirements>
+    <version_command>PretextMap --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $input.is_of_type("bam"):
+            samtools view -h '${input}' |
+        #else
+            cat '${input}' |
+        #end if
+        PretextMap
+        #if $sorting.sortby == "length":
+            --sortby length
+            --sortorder $sorting.sortorder
+        #elif $sorting.sortby == "name":
+            --sortby name
+            --sortorder $sorting.sortorder
+        #end if
+        #if $map_qual:
+            --mapq $map_qual
+        #end if
+        #if $filter.filter_type == "in":
+            --filterInclude '$filter.filter_list'
+        #elif $filter.filter_type == "out":
+            --filterExclude '$filter.filter_list'
+        #end if 
+        -o output.pretext
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="sam,bam" label="Input dataset in SAM or BAM format"/>
+        <conditional name="sorting">
+            <param argument="--sortby" type="select" label="Sort by">
+                <option value="nosort" selected="true">Don't sort</option>
+                <option value="length">Length</option>
+                <option value="name">Name</option>
+            </param>
+            <when value="nosort"/>
+            <when value="length">
+                <param argument="--sortorder" type="select" label="Sort order: ">
+                    <option value="ascend">Ascending</option>
+                    <option value="decend">Decending</option>
+                </param>
+            </when>
+            <when value="name">
+                <param argument="--sortorder" type="select" label="Sort order: ">
+                    <option value="ascend">Ascending</option>
+                    <option value="descend">Decending</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="map_qual" type="integer" label="Minimum mapping quality:" min="0" optional="true"/>
+        <conditional name="filter">
+            <param name="filter_type" type="select" label="How to filter: ">
+                <option value="" selected="true">No filter</option>
+                <option value="in">Filter to include only specified sequence names</option>
+                <option value="out">Filter to exclude specified sequence names</option>
+            </param>
+            <when value=""/>
+            <when value="in">
+                <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1, seq_2">
+                    <sanitizer>
+                        <valid initial="string.ascii_letters,string.digits">
+                            <add value="_"/>
+                        </valid>
+                    </sanitizer>
+                </param>
+            </when>
+            <when value="out">
+                <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1, seq_2">
+                    <sanitizer>
+                        <valid initial="string.ascii_letters,string.digits">
+                            <add value="_"/>
+                        </valid>
+                    </sanitizer>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="pretext" name="pretext_map_out" from_work_dir="output.pretext" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="bam" value="test.bam"/>
+            <conditional name="sorting">
+                <param name="sortby" value="length"/>
+                <param name="sortorder" value="ascend"/>
+            </conditional>
+            <conditional name="filter">
+                <param name="filter_type" value="in"/>
+                <param name="filter_list" value="ref"/>
+            </conditional>
+            <param name="map_qual" value="10"/>
+            <output name="pretext_map_out" file="output_1.pretext"/>
+        </test>
+        <test>
+            <param name="input" ftype="sam" value="test.sam"/>
+            <conditional name="sorting">
+                <param name="sortby" value="name"/>
+                <param name="sortorder" value="descend"/>
+            </conditional>
+            <conditional name="filter">
+                <param name="filter_type" value="out"/>
+                <param name="filter_list" value="chrM, chr8, chr9"/>
+            </conditional>
+            <output name="pretext_map_out" file="output_2.pretext"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What is does**
+
+The Paired REad TEXTure Mapper converts aligned read pairs into genome contact maps.
+Pretext has no special requirement on the alignment files
+process your alignments however you want before feeding to PretextMap.
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @misc{Harry_et_al,
+            Author={Harry, E},
+            title={Paired REad TEXTure Snapshot: Command line image generator for Pretext contact maps.},
+            url = {https://github.com/wtsi-hpag/PretextSnapshot},}
+        </citation>
+    </citations>
+</tool>