--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chira_quantify.xml	Sun Jan 19 16:29:48 2020 -0500
@@ -0,0 +1,64 @@
+<tool id="chira_quantify" name="ChiRA qauntify" version="@WRAPPER_VERSION@0">
+    <description>quantify aligned loci to score the alignments</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command><![CDATA[
+        chira_quantify.py
+        -b '$segments'
+        -m '$merged'
+        -cs '$crl_share'
+        -ls '$min_locus_size'
+        -e '$em_threshold'
+        '$crl'
+        -o ./
+    ]]></command>
+
+    <inputs>
+        <param format="bed" name="segments" type="data" label="BED file of aligned segments"/>
+        <param format="tabular" name="merged" type="data" label="Tabular file of merged alignments"/>
+        <param name="crl_share" type="float" value="0.7" label="CRL locus fraction" min="0" max="1"
+            help="Minimum fraction of reads of a locus that must overlap with all CRL loci inorder to merge itinto that CRL."/>
+        <param name="min_locus_size" type="integer" value="5" label="Minimum locus size" min="1"
+            help="Minimum number of reads a locus should have in order to participate in CRL creation.
+                 Always set this value relative to your sequencing depth. Setting this to lower leads
+                 CRLs of random multimappings Also consider setting the --crl_share option
+                 along with this"/>
+       <param name="em_threshold" type="float" value="1" label="EM threshold"
+              help="The maximum difference of transcripts expression between two consecutive iterations of EM algorithm to converge."/>
+       <param name="crl" type="boolean" truevalue="-crl" falsevalue="" checked="true"
+              label="Create CRLs" help="Create CRLs and qunatify them or use the loci further without creating the CRLs" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="loci" from_work_dir="loci.counts" label="ChiRA quantified loci on ${on_string}"/>
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="segments" value="segments.bed"/>
+            <param name="merged" value="merged.bed"/>
+            <output name="loci" file="loci.counts"/>
+        </test>
+    </tests>
+
+    <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool first creates CRLS from merged BED file and quantifies them based on the mapped reads.
+
+**Inputs**
+
+  * A BED file containing alignment segments
+  * A BED file containing merged alignments
+
+**Output**
+
+  * Tabular file containing the reads and their CRLs with TPM values.
+
+    </help>
+    <expand macro="citations" />
+  </tool>