--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate-putative-usp.xml	Mon Jun 05 02:51:59 2023 +0000
@@ -0,0 +1,122 @@
+<tool id="edu.tamu.cpt2.spanin.generate-putative-usp" name="USP Candidates" version="1.0">
+    <description>constructs a putative list of potential u-spanin from an input genomic FASTA</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>cpt-macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+    </expand>
+    <command detect_errors="aggressive"><![CDATA[
+python '$__tool_directory__/generate-putative-usp.py'
+'$fa'
+--strand '$strand'
+--min_size '$min_size'
+--max_size '$max_size'
+--lipo_min_start '$lipo_min_start'
+--lipo_max_start '$lipo_max_start'
+--min_lipo_after '$min_lipo_after'
+--max_lipo_after '$max_lipo_after'
+--tmd_min_start '$tmd_min_start'
+--tmd_max_start '$tmd_max_start'
+--tmd_min_size '$tmd_min_size'
+--tmd_max_size '$tmd_max_size'
+--putative_usp_gff '$putative_usp_gff'
+--summary_usp_txt '$summary_usp'
+--putative_usp '$putative_usp'
+--usp_og '$usp_og'
+--usp_ob '$usp_ob'
+--usp_op '$usp_op'
+--usp_on '$usp_on'
+--switch '$switch'
+    ]]></command>
+    <inputs>
+        <param label="FASTA" name="fa" type="data" format="fasta"/>
+        <param type="select" label="Strand Choice" name="strand">
+            <option value="both">both</option>
+            <option value="forward">+</option>
+            <option value="reverse">-</option>
+        </param>
+        <param label="u-spanin minimal length" type="integer" name="min_size" value="100"/>
+        <param label="u-spanin maximum length" type="integer" name="max_size" value="200"/>
+        <param label="Range Selection; default is all; slices are based on NT. Separated by a colon (eg. #:#)" name="switch" type="text" value="all"/>
+        <param label="TMD minimal distance from start codon" type="integer" name="tmd_min_start" value="75"/>
+        <param label="TMD maximum distance from start codon" type="integer" name="tmd_max_start" value="200"/>
+        <param label="TMD minimal size" type="integer" name="tmd_min_size" value="15"/>
+        <param label="TMD maximum size" type="integer" name="tmd_max_size" value="25"/>
+        <param label="Lipobox minimal distance from start codon" type="integer" name="lipo_min_start" value="10"/>
+        <param label="Lipobox maximum distance from start codon" type="integer" name="lipo_max_start" value="30"/>
+        <param label="Minimum amount of periplasmic residues after Lipobox" type="integer" name="min_lipo_after" value="60"/>
+        <param label="Maximum amount of periplasmic residues after Lipobox" type="integer" name="max_lipo_after" value="160"/>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="usp_on" label="NucSequences.fa" hidden="true"/>
+        <data format="fasta" name="usp_op" label="ProtSequences.fa" hidden="true"/>
+        <data format="bed" name="usp_ob" label="BED_Output.bed" hidden="true"/>
+        <data format="gff3" name="usp_og" label="GFF_Output.gff" hidden="true"/>
+        <data format="fasta" name="putative_usp" label="putative_usp.fa"/>
+        <data format="txt" name="summary_usp" label="summary_usp.txt"/>
+        <data format="gff3" name="putative_usp_gff" label="putative_usp.gff3"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fa" value="t1.fa"/>
+            <param name="min-size" value="100"/>
+            <param name="max-size" value="200"/>
+            <param name="switch" value="all"/>
+            <param name="tmd_min_start" value="75"/>
+            <param name="tmd_max_start" value="200"/>
+            <param name="tmd_min_size" value="15"/>
+            <param name="tmd_max_size" value="25"/>
+            <param name="lipo_min_start" value="15"/>
+            <param name="lipo_max_start" value="30"/>
+            <param name="min_lipo_after" value="60"/>
+            <param name="max_lipo_after" value="160"/>
+            <param name="select" value="1"/>
+            <output name="usp_on" file="_out_usp.fna"/>
+            <output name="usp_op" file="_out_usp.fa"/>
+            <output name="usp_ob" file="_out_usp.bed"/>
+            <output name="usp_og" file="_out_usp.gff3"/>
+            <output name="putative_usp" file="_putative_usp.fa"/>
+            <output name="summary_usp" file="_summary_usp.txt"/>
+            <output name="putative_usp_gff" file="_putative_usp.gff3"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+Searches a genome for candidate u-spanins (USPs), a phage protein involved in outer membrane disruption during Gram-negative bacterial host cell lysis. 
+
+
+**METHODOLOGY**
+This tool combines the methods used in the ISP and OSP Candidates tools to search for putative transmembrane domains and lipoboxes. See those tools for additional detail. Within user-set parameters, the following residues are allowed:
+
+Hydrophobic residues allowed in TMD:
+
+    * [FIWLVMYCATGSP]
+
+Lipobox patterns:
+
+    * [ILMFTV][^REKD][GAS]C
+    * A W[AGS]C
+
+**INPUT** --> Genomic FASTA
+*Note* - Use a single genome fasta. Multiple FASTAs will not work.
+
+**OUTPUT** -->
+Protein sequences which passed the above filters are returned as the candidate USPs in three files: a protein FASTA file, a GFF3, and basic summary statistics text file.
+.
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1371/journal.pcbi.1008214</citation>
+        <citation type="doi">https://dx.doi.org/10.1016/bs.aivir.2018.09.003</citation>
+        <citation type="bibtex">
+            @unpublished{galaxyTools,
+            author = {C. Ross},
+            title = {CPT Galaxy Tools},
+            year = {2020-},
+            note = {https://github.com/tamu-cpt/galaxy-tools/}
+            }
+        </citation>
+    </citations>
+</tool>