--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cryptogenotyper.xml	Fri Oct 16 02:23:24 2020 +0000
@@ -0,0 +1,141 @@
+<tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@">
+  <description>
+    CryptoGenotyper is a standalone tool to analyze Cryptosporidium Sanger sequencing data and classify the species and subtype based on SSU rRNA and gp60 gene markers, respectively.
+  </description>
+  <macros>
+   <token name="@VERSION@">1.0</token>
+  </macros>
+  <requirements>
+    <requirement type="package" version ="@VERSION@">cryptogenotyper</requirement>
+  </requirements>
+  <version_command>cryptogenotyper --version</version_command>
+  <command detect_errors="exit_code">
+     <![CDATA[
+
+     #set $ref_file=''
+
+     #if $reference.ref == "no"
+        ln -s "${reference.db}" "${reference.db.name}" &&
+        #set $ref_file = $reference.db.name
+     #end if
+
+     #if $primers["seqtype"] == "contig"
+        ln -s "${$primers.abi_input["forward"]}" "${primers.abi_input.name}_forward.ab1" &&
+        ln -s "${$primers.abi_input["reverse"]}" "${primers.abi_input.name}_reverse.ab1" &&
+        cryptogenotyper -i "." -m "$marker" -t "$primers.seqtype" -f "forward" -r "reverse"
+        #if $reference.ref == "no"
+          --databasefile $ref_file
+        #end if
+     #else
+        ln -s "${primers.abi_input}" "${primers.abi_input.element_identifier}" &&
+        cryptogenotyper -i "./${primers.abi_input.element_identifier}" -m "$marker" -t "$primers.seqtype" -f "" -r ""
+        #if $reference.ref == "no"
+          --databasefile $ref_file
+        #end if
+     #end if
+     #if $outputheader == "no"
+           --noheaderline
+     #end if
+     -o "result";
+     ]]>
+  </command>
+  <inputs>
+      <param name="marker" type="select" label="Marker">
+          <option value="18S">SSU rRNA</option>
+          <option value="gp60">gp60</option>
+      </param>
+      <conditional name="reference">
+        <param name="ref" type="select" label="Use default reference file?">
+            <option value="yes">Yes</option>
+            <option value="no">No</option>
+        </param>
+        <when value="yes">
+        </when>
+        <when value="no">
+            <param name="db" type="data" format="fasta" label="Reference Database File:" help=".fa fasta file type"/>
+        </when>
+      </conditional>
+      <conditional name="primers">
+        <param name="seqtype" type="select" label="Type of Sequences">
+            <option value="forward">Forward Only</option>
+            <option value="reverse">Reverse Only</option>
+            <option selected="true" value="contig">Contig</option>
+        </param>
+        <when value="contig">
+          <param name="abi_input" type="data_collection" collection_type="paired" format="ab1" label="Paired Sequencing File(s)" help=".ab1 file type"/>
+        </when>
+        <when value="forward">
+          <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)" help=".ab1 file type"/>
+        </when>
+        <when value="reverse">
+          <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)" help=".ab1 file type"/>
+        </when>
+     </conditional>
+     <param name="outputheader" type="select" value="yes" label="Output header line in the report?">
+        <option value="yes">Yes</option>
+        <option value="no">No</option>
+     </param>
+
+
+  </inputs>
+  <outputs>
+    <data name="outfile" format="fasta" from_work_dir="result_cryptogenotyper_report.fa" label="${tool.name}:${on_string}:fastas"/>
+    <data name="outfile_report" format="tabular" from_work_dir="result_cryptogenotyper_report.txt" label="${tool.name}:${on_string}:reports"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="marker" value="18S"/>
+      <param name="seqtype" value="forward"/>
+      <param name="abi_input" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/>
+      <output name="outfile_report" ftype="tabular">
+          <assert_contents>
+              <has_text_matching expression="C.parvum"/>
+          </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="marker" value="gp60"/>
+      <param name="seqtype" value="forward"/>
+      <param name="abi_input"  value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/>
+      <output name="outfile_report" ftype="tabular" >
+          <assert_contents>
+              <has_text_matching expression="C.parvum"/>
+          </assert_contents>
+      </output>
+    </test>
+  </tests>
+
+
+  <help>
+
+
+**Syntax**
+
+CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.
+For more information please visit https://github.com/phac-nml/CryptoGenotyper.
+
+-----
+
+**Input:**
+
+AB1 file(s) representing *Cryptosporidium's* SSU rRNA or gp60 locus (forward, reverse, or contig (forward and reverse paired-end reads)).
+Optional: A custom reference database in .fa file format, to be used during the homology search for *Cryptosporidium* classification.
+
+
+**Output:**
+
+FASTA file containing the identification of the *Cryptosporidium* species/subtype and its corresponding sequence for each sample.
+  </help>
+  <citations>
+    <citation type="bibtex">
+  @misc{githubCryptoGenotyper,
+  author = {Yanta C, Bessonov K, Robinson G, Troell K, Guy R},
+  title = {CryptoGenotyper: a new bioinformatics tool to enhance Cryptosporidium identification},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/phac-nml/CryptoGenotyper}
+    }</citation>
+  </citations>
+
+</tool>