--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uniprot.xml	Fri Oct 09 16:42:22 2015 -0400
@@ -0,0 +1,355 @@
+<tool id="uniprot" name="UniProt" version="0.1">
+    <description>ID mapping and retrieval</description>
+    <macros>
+         <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="2.7">requests</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
+    <version_command>echo "UniProt ID mapping for Galaxy in version 0.1"</version_command>
+    <command><![CDATA[
+
+        cut -f ${id_column} $infile > id_file.tabular &&
+
+        $__tool_directory__/uniprot.py
+
+        #if $tool.tool_choice == "retrieve":
+            retrieve -f $tool.format $infile ./output
+        #elif $tool.tool_choice == "map":
+            map
+
+            #if $tool.from.category_FROM == "uniprot":
+                $tool.from.db_uniprot_FROM
+            #elif $tool.from.category_FROM == "oseqdb":
+                $tool.from.db_oseqdb
+            #elif $tool.from.category_FROM == "3Dstrdb":
+                $tool.from.db_3Dstrdb
+            #elif $tool.from.category_FROM == "ppidb":
+                $tool.from.db_ppidb
+            #elif $tool.from.category_FROM == "chemistry":
+                $tool.from.db_chemistry
+            #elif $tool.from.category_FROM == "protfgdb":
+                $tool.from.db_protfgdb
+            #elif $tool.from.category_FROM == "polymorphismANDmutation":
+                $tool.from.db_polymorphismANDmutation
+            #elif $tool.from.category_FROM == "db_2DgelDB":
+                $tool.from.db_2DgelDB
+            #elif $tool.from.category_FROM == "ProtocolsMaterialsDB":
+                $tool.from.ProtocolsMaterialsDB
+            #elif $tool.from.category_FROM == "db_GenomeAnnotationDB":
+                $tool.from.db_GenomeAnnotationDB
+            #elif $tool.from.category_FROM == "db_OrganismSpecificGeneDB":
+                $tool.from.db_OrganismSpecificGeneDB
+            #elif $tool.from.category_FROM == "db_phylogenomic":
+                $tool.from.db_phylogenomic
+            #elif $tool.from.category_FROM == "db_EnzymePathwayDB":
+                $tool.from.db_EnzymePathwayDB
+            #elif $tool.from.category_FROM == "db_GeneExpression":
+                $tool.from.db_GeneExpression
+            #elif $tool.from.category_FROM == "db_other":
+                $tool.from.db_other
+            #end if
+
+            #if $tool.to.category_TO == "uniprot":
+                $tool.to.db_uniprot_TO
+            #elif $tool.to.category_TO == "oseqdb":
+                $tool.to.db_oseqdb
+            #elif $tool.to.category_TO == "3Dstrdb":
+                $tool.to.db_3Dstrdb
+            #elif $tool.to.category_TO == "ppidb":
+                $tool.to.db_ppidb
+            #elif $tool.to.category_TO == "chemistry":
+                $tool.to.db_chemistry
+            #elif $tool.to.category_TO == "protfgdb":
+                $tool.to.db_protfgdb
+            #elif $tool.to.category_TO == "polymorphismANDmutation":
+                $tool.to.db_polymorphismANDmutation
+            #elif $tool.to.category_TO == "db_2DgelDB":
+                $tool.to.db_2DgelDB
+            #elif $tool.to.category_TO == "ProtocolsMaterialsDB":
+                $tool.to.ProtocolsMaterialsDB
+            #elif $tool.to.category_TO == "db_GenomeAnnotationDB":
+                $tool.to.db_GenomeAnnotationDB
+            #elif $tool.frtoom.category_TO == "db_OrganismSpecificGeneDB":
+                $tool.to.db_OrganismSpecificGeneDB
+            #elif $tool.to.category_TO == "db_phylogenomic":
+                $tool.to.db_phylogenomic
+            #elif $tool.to.category_TO == "db_EnzymePathwayDB":
+                $tool.to.db_EnzymePathwayDB
+            #elif $tool.to.category_TO == "db_GeneExpression":
+                $tool.to.db_GeneExpression
+            #elif $tool.to.category_TO == "db_other":
+                $tool.to.db_other
+            #end if
+
+            id_file.tabular
+            ./output
+        #end if
+
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="tabular" label="Input file with IDs"
+            help="One ID in each line."/>
+        <param name="id_column" label="ID column" type="data_column" data_ref="infile" help=""/>
+
+        <conditional name="tool">
+            <param name="tool_choice" type="select" label="Do you want to map IDs or retrieve data from UniProt" help="">
+                <option value="retrieve">Retrieve: request entries by uniprot accession using batch retrieval</option>
+                <option value="map" selected="True">Map: map a list of ids from one format onto another using uniprots mapping API</option>
+            </param>
+            <when value="map">
+                <conditional name="from">
+                    <expand macro="macro-category_FROM"/>
+                    <when value="uniprot">
+                        <expand macro="macro-db_uniprot_FROM"/>
+                    </when>
+                    <when value="oseqdb">
+                        <expand macro="macro-db_oseqdb"/>
+                    </when>
+                    <when value="3Dstrdb">
+                        <expand macro="macro-db_3Dstrdb"/>
+                    </when>
+                    <when value="ppidb">
+                        <expand macro="macro-db_ppidb"/>
+                    </when>
+                    <when value="chemistry">
+                        <expand macro="macro-db_chemistry"/>
+                    </when>
+                    <when value="protfgdb">
+                        <expand macro="macro-db_protfgdb"/>
+                    </when>
+                    <when value="polymorphismANDmutation">
+                        <expand macro="macro-db_polymorphismANDmutation"/>
+                    </when>
+                    <when value="2DgelDB">
+                        <expand macro="macro-db_2DgelDB"/>
+                    </when>
+                    <when value="ProtocolsMaterialsDB">
+                        <expand macro="macro-db_ProtocolsMaterialsDB"/>
+                    </when>
+                    <when value="GenomeAnnotationDB">
+                        <expand macro="macro-db_GenomeAnnotationDB"/>
+                    </when>
+                    <when value="OrganismSpecificGeneDB">
+                        <expand macro="macro-db_OrganismSpecificGeneDB"/>
+                    </when>
+                    <when value="phylogenomic">
+                        <expand macro="macro-db_phylogenomic"/>
+                    </when>
+                    <when value="EnzymePathwayDB">
+                        <expand macro="macro-db_EnzymePathwayDB"/>
+                    </when>
+                    <when value="GeneExpression">
+                        <expand macro="macro-db_GeneExpression"/>
+                    </when>
+                    <when value="other">
+                        <expand macro="macro-db_other"/>
+                    </when>
+                </conditional>
+                <conditional name="to">
+                    <expand macro="macro-category_TO"/>
+                    <when value="uniprot">
+                        <expand macro="macro-db_uniprot_TO"/>
+                    </when>
+                    <when value="oseqdb">
+                        <expand macro="macro-db_oseqdb"/>
+                    </when>
+                    <when value="3Dstrdb">
+                        <expand macro="macro-db_3Dstrdb"/>
+                    </when>
+                    <when value="ppidb">
+                        <expand macro="macro-db_ppidb"/>
+                    </when>
+                    <when value="chemistry">
+                        <expand macro="macro-db_chemistry"/>
+                    </when>
+                    <when value="protfgdb">
+                        <expand macro="macro-db_protfgdb"/>
+                    </when>
+                    <when value="polymorphismANDmutation">
+                        <expand macro="macro-db_polymorphismANDmutation"/>
+                    </when>
+                    <when value="2DgelDB">
+                        <expand macro="macro-db_2DgelDB"/>
+                    </when>
+                    <when value="ProtocolsMaterialsDB">
+                        <expand macro="macro-db_ProtocolsMaterialsDB"/>
+                    </when>
+                    <when value="GenomeAnnotationDB">
+                        <expand macro="macro-db_GenomeAnnotationDB"/>
+                    </when>
+                    <when value="OrganismSpecificGeneDB">
+                        <expand macro="macro-db_OrganismSpecificGeneDB"/>
+                    </when>
+                    <when value="phylogenomic">
+                        <expand macro="macro-db_phylogenomic"/>
+                    </when>
+                    <when value="EnzymePathwayDB">
+                        <expand macro="macro-db_EnzymePathwayDB"/>
+                    </when>
+                    <when value="GeneExpression">
+                        <expand macro="macro-db_GeneExpression"/>
+                    </when>
+                    <when value="other">
+                        <expand macro="macro-db_other"/>
+                    </when>
+                </conditional>
+            </when>
+            <when value="retrieve">
+                <param name="format" type="select" label="Choose format of output file" help="">
+                    <option value="fasta">fasta</option>
+                    <option value="gff">gff</option>
+                </param>
+            </when>
+        </conditional>
+
+    </inputs>
+    <outputs>
+            <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output"
+                label="${tool.name} on ${on_string} (retrieve output)">
+                <filter>tool['tool_choice'] == 'retrieve'</filter>
+                <filter>tool['format'] == 'fasta'</filter>
+            </data>
+            <data name="outfile_retrieve_gff" format="gff" from_work_dir="./output"
+                label="${tool.name} on ${on_string} (retrieve output)">
+                <filter>tool['tool_choice'] == 'retrieve'</filter>
+                <filter>tool['format'] == 'gff'</filter>
+            </data>
+            <data name="outfile_map" format="tabular" from_work_dir="./output"
+                label="${tool.name} on ${on_string} (map output)">
+                <filter>tool['tool_choice'] == 'map'</filter>
+            </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
+            <param name="id_column" value="c1"/>
+            <param name="format" value="fasta"/>
+            <param name="tool_choice" value="retrieve"/>
+            <output name="outfile_retrieve" file="test1_retrieve.fasta" ftype="fasta"/>
+        </test>
+        <test>
+            <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
+            <param name="id_column" value="c1"/>
+            <param name="format" value="gff"/>
+            <param name="tool_choice" value="retrieve"/>
+            <output name="outfile_retrieve" file="test2_retrieve.gff" ftype="gff"/>
+        </test>
+        <test>
+            <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
+            <param name="id_column" value="c1"/>
+            <param name="tool_choice" value="map"/>
+            <param name="category_FROM" value="uniprot"/>
+            <param name="db_uniprot_FROM" value="ID"/>
+            <param name="category_TO" value="uniprot"/>
+            <param name="db_uniprot_TO" value="GENENAME"/>
+            <output name="outfile_map" file="test1_map.tab" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="infile" value="id_map_refseq.txt" ftype="tabular"/>
+            <param name="id_column" value="c1"/>
+            <param name="tool_choice" value="map"/>
+            <param name="category_FROM" value="oseqdb"/>
+            <param name="db_oseqdb" value="REFSEQ_NT_ID"/>
+            <param name="category_TO" value="uniprot"/>
+            <param name="db_uniprot_TO" value="ID"/>
+            <output name="outfile_map" file="test2_map.tab" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does** 
+
+This tool provides access to the UniProt API. You can retrieve sequence informations given a list of sequence identifiers or map
+identifiers between different databases.
+Hence, this tool offers you two modes: *map* and *retrieve*.
+
+-----
+
+**INPUT**
+
+The input is a list of IDs.
+
+*example*:
+
+Q0P8A9
+A0A077ZHN8
+A0A077ZFY8
+M5B8V9
+M5BAG7
+S0DS17
+....
+
+-----
+
+**MAP OUTPUT EXAMPLES**
+
+FROM refseq TO embl::
+
+    From    To
+    NM_130786    A1BG_HUMAN
+    NM_130786    V9HWD8_HUMAN
+    NM_001087    A0A024R410_HUMAN
+    NM_001087    AAMP_HUMAN
+    
+FROM uniprot TO genename::
+
+    From        To
+    Q0P8A9      fdhC
+    A0A077ZHN8  TTRE_0000819801
+    A0A077ZFY8  TTRE_0000758701
+    M5B8V9      CMN_01519
+    M5BAG7      cydC
+    S0DS17      FFUJ_00006
+    A0A077Z587  TTRE_0000309301
+    Q13685      AAMP
+    O14639      ABLIM1
+
+-----
+
+**RETRIEVE OUTPUT EXAMPLES**
+
+retrieve gff::
+
+    #gff-version 3
+    #sequence-region S0DS17 1 369
+    #sequence-region M5BAG7 1 563
+    #sequence-region A0A077Z587 1 772
+    #sequence-region A0A077ZFY8 1 973
+    #sequence-region O14639 1 778
+    O14639	UniProtKB	Chain	1	778	.	.	.	ID=PRO_0000075697;Note=Actin-binding LIM protein 1	
+    O14639	UniProtKB	Domain	97	156	.	.	.	Note=LIM zinc-binding 1;evidence=ECO:0000255|PROSITE-ProRule:PRU00125	
+    O14639	UniProtKB	Domain	156	216	.	.	.	Note=LIM zinc-binding 2;evidence=ECO:0000255|PROSITE-ProRule:PRU00125	
+    O14639	Un...
+
+retrieve fasta::
+
+    >tr|S0DS17|S0DS17_GIBF5 Related to cytochrom P450 OS=Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) GN=FFUJ_00006 PE=3 SV=1
+    MSYQSILLRQVNSLCDNLEEVARDENGGLIDMAMQSDYFTFDVMSEVIFGMAYNALKDTS
+    YRFVTGALGSSNIRIGTLVQSPLPAMCRIDKY...
+    >tr|M5BAG7|M5BAG7_9MICO ABC transporter, fused permease/ABC transporter involved in the biosynthesis of cytochrom bd, fused permease/ATP-binding protein OS=Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 GN=cydC PE=3 SV=1
+    MNRDGVLRLAQPPTRRTLPGLLAGLASAVGAVALLATSAWLITRASEQPPILFLGMAIVG
+    VRAFALGRAAFRYLERITSHDAAFRALATLRV...
+    >tr|A0A077Z587|A0A077Z587_TRITR Kelch 3 and Kelch 4 and Cytochrom B561 domain con taining protein OS=Trichuris trichiura GN=TTRE_0000309301 PE=4 SV=1
+    MGSQQAADETQKVVERIILNINVRKDKRSFGLGIKIKKGNVFVSSIRPGSIAEDHFKLYD
+    VIKDVNGSRIDSRELCRDLIRTHKVLTV...
+
+-----
+
+This tool is based on the work `Jan Rudolph`_ and the UniProt API.
+
+.. _Jan Rudolph: https://github.com/jdrudolph/uniprot
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/nar/gku989</citation>
+    </citations>
+</tool>