--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/unipept.xml	Wed Oct 24 14:45:18 2018 -0400
@@ -0,0 +1,518 @@
+<tool id="unipept" name="Unipept" version="4.0.0">
+    <description>retrieve taxonomy for peptides</description>
+    <macros>
+        <xml name="equate_il">
+            <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine">
+                <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help>
+            </param>
+        </xml>
+        <xml name="extra">
+            <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="false" label="retrieve extra information">
+                <yield/>
+            </param>
+        </xml>
+        <xml name="extra_true">
+            <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="true" label="retrieve extra information">
+                <yield/>
+            </param>
+        </xml>
+        <xml name="names">
+            <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" >
+                <help>return the names in complete taxonomic lineage</help>
+            </param>
+            <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields" >
+                <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help>
+            </param>
+        </xml>
+        <xml name="domains">
+            <param name="domains" type="boolean" truevalue="-D" falsevalue="" checked="false" label="group responses by GO namespace (biological process, molecular function, cellular component)">
+                <yield/>
+            </param>
+        </xml>
+        <xml name="selected_outputs">
+            <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
+                <option value="tsv" selected="true">Tabular with one line per peptide</option>
+                <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
+                <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
+                <yield/>
+                <option value="unmatched">Unmatched peptides</option>
+            </param>
+        </xml>
+    </macros>
+    <requirements>
+        <requirement type="package" version="2.7">python</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+      python '$__tool_directory__/unipept.py' 
+      ## --url 'http://morty.ugent.be/api/v1' -g -M 1  
+      --api=$unipept.api
+      $unipept.equate_il $unipept.extra 
+      #if $unipept.api in ['pept2lca', 'pept2taxa', 'peptinfo']:
+        $unipept.names $unipept.allfields
+      #end if
+      #if $unipept.api in ['pept2go', 'pept2funct', 'peptinfo']:
+        $unipept.domains
+      #end if
+      $strict
+      #if str($peptide_src.fmt) == 'proteomic':
+        #if $peptide_src.input.datatype.file_ext == 'fasta':
+          --fasta="$peptide_src.input"
+        #elif $peptide_src.input.datatype.file_ext == 'mzid':
+          --mzid="$peptide_src.input"
+        #elif $peptide_src.input.datatype.file_ext == 'pepxml':
+          --pepxml="$peptide_src.input"
+        #end if
+      #elif str($peptide_src.fmt) == 'tabular':
+        --tabular="$peptide_src.input_tsv"
+        #set $col = int(str($peptide_src.column)) - 1
+        --column=$col
+      #elif str($peptide_src.fmt) == 'fasta':
+        --fasta="$peptide_src.input_fasta"
+      #elif str($peptide_src.fmt) == 'mzid':
+        --mzid="$peptide_src.input_mzid"
+      #elif str($peptide_src.fmt) == 'pepxml':
+        --pepxml="$peptide_src.input_pepxml"
+      #end if
+      #if 'json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2lca', 'pept2taxa', 'peptinfo']:
+        --json $output_json
+      #end if
+      #if 'ec_json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
+        --ec_json $output_ec_json
+      #end if
+      #if 'tsv' in str($selected_outputs).split(','):
+        --tsv $output_tsv
+      #end if
+      #if 'csv' in str($selected_outputs).split(','):
+        --csv $output_csv
+      #end if
+      #if 'ec_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
+        --ec_tsv $output_ec_tsv
+      #end if
+      #if 'go_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2go', 'pept2funct', 'peptinfo']:
+        --go_tsv $output_go_tsv
+      #end if
+      #if 'unmatched' in str($selected_outputs).split(','):
+        --unmatched $output_unmatched
+      #end if
+    ]]></command>
+    <inputs>
+      <conditional name="unipept">
+          <param name="api" type="select" label="Unipept application" >
+              <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>
+              <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>
+              <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option>
+              <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option>
+              <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option>
+              <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option>
+              <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option>
+          </param>
+          <when value="pept2lca">
+              <expand macro="equate_il" />
+              <expand macro="extra">
+                  <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help>
+              </expand>
+              <expand macro="names" />
+          </when>
+          <when value="pept2taxa">
+              <expand macro="equate_il" />
+              <expand macro="extra_true">
+                  <help>Return the complete lineage of each organism, and include ID fields.</help>
+              </expand>
+              <expand macro="names" />
+          </when>
+          <when value="pept2prot">
+              <expand macro="equate_il" />
+              <expand macro="extra">
+                  <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids
+                        WARNING: Huge perfomance penalty!  Only use for small number of peptides when the extra infomation is required.
+                  </help>
+              </expand>
+          </when>
+          <when value="pept2ec">
+              <expand macro="equate_il" />
+              <expand macro="extra_true">
+                  <help>Return the name of the EC-number.
+                  </help>
+              </expand>
+          </when>
+          <when value="pept2go">
+              <expand macro="equate_il" />
+              <expand macro="extra_true">
+                  <help>Return the name of the GO-term.
+                  </help>
+              </expand>
+              <expand macro="domains" />
+          </when>
+          <when value="pept2funct">
+              <expand macro="equate_il" />
+              <expand macro="extra_true">
+                  <help>Return the name of the  EC-number and GO-term.
+                  </help>
+              </expand>
+              <expand macro="domains" />
+          </when>
+          <when value="peptinfo">
+              <expand macro="equate_il" />
+              <expand macro="extra_true">
+                  <help>Return the name of the  EC-number and GO-term.
+                  </help>
+              </expand>
+              <expand macro="domains" />
+              <expand macro="names" />
+          </when>
+      </conditional>
+      <conditional name="peptide_src">
+        <param name="fmt" type="select" label="Peptides input format" >
+          <option value="proteomic">proteomics formats:  mzid, pepxml, fasta</option>
+          <option value="tabular">tabular</option>
+          <option value="fasta">fasta</option>
+          <option value="mzid">mzid</option>
+          <option value="pepxml">pepxml</option>
+        </param>
+        <when value="proteomic">
+          <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input" />
+        </when>
+        <when value="tabular">
+          <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column" />
+          <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv" />
+        </when>
+        <when value="fasta">
+          <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input" />
+        </when>
+        <when value="mzid">
+          <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input" />
+        </when>
+        <when value="pepxml">
+          <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" />
+        </when>
+      </conditional>
+      <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
+       <option value="tsv" selected="true">Tabular with one line per peptide</option>
+       <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
+        <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
+        <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option>
+        <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option>
+        <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option>
+        <option value="unmatched">Unmatched peptides</option>
+      </param>
+      <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/>
+    </inputs>
+    <outputs>
+      <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} Taxonomy json"> 
+        <filter>'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo')</filter>
+        <change_format>
+            <when input="api" value="pept2prot" format="json" />
+        </change_format>
+      </data> 
+      <data name="output_ec_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} EC json">
+        <filter>'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
+      </data>
+      <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv"> 
+        <filter>'tsv' in selected_outputs</filter>
+        <actions>
+            <action name="comment_lines" type="metadata" default="1" />
+            <!--
+            <conditional name="unipept.api">
+                <when value="pept2funct">
+                    <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names,go_terms,go_protein_counts,go_names" />
+                </when>
+                <when value="pept2go">
+                    <action name="column_names" type="metadata" default="peptide,total_protein_count,go_terms,go_protein_counts,go_names" />
+                </when>
+                <when value="pept2ec">
+                    <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names" />
+                </when>
+            </conditional>
+            -->
+        </actions>
+peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names,go_terms,go_protein_counts,go_names
+      </data> 
+      <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv"> 
+        <filter>'csv' in selected_outputs</filter>
+      </data> 
+      <data name="output_ec_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} EC tsv"> 
+        <filter>'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
+        <actions>
+            <action name="column_names" type="metadata" default="Peptide,Total Protein Count,EC Number,Protein Count,EC Name" />
+        </actions>
+      </data> 
+      <data name="output_go_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} GO tsv"> 
+        <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter>
+        <actions>
+            <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name" />
+        </actions>
+      </data> 
+      <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched"> 
+        <filter>'unmatched' in selected_outputs</filter>
+        <actions>
+            <action name="column_names" type="metadata" default="Unmatched Peptide" />
+        </actions>
+      </data> 
+    </outputs>
+    <tests>
+      <test>
+        <param name="api" value="pept2lca"/>
+        <param name="fmt" value="tabular"/>
+        <param name="input_tsv" value="tryptic.tsv"/>
+        <param name="column" value="2"/>
+        <param name="extra" value="True"/>
+        <param name="names" value="True"/>
+        <param name="selected_outputs" value="tsv,unmatched"/>
+        <output name="output_tsv">
+            <assert_contents>
+              <has_text text="Homininae" />
+            </assert_contents>
+        </output>
+        <output name="output_unmatched">
+            <assert_contents>
+              <has_text text="QTAMAV" />
+            </assert_contents>
+        </output>
+      </test>
+      <test>
+        <param name="api" value="pept2lca"/>
+        <param name="fmt" value="fasta"/>
+        <param name="input_fasta" value="peptide.fa"/>
+        <param name="equate_il" value="True"/>
+        <param name="extra" value="True"/>
+        <param name="names" value="True"/>
+        <param name="selected_outputs" value="json,tsv"/>
+        <output name="output_json">
+            <assert_contents>
+              <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" />
+            </assert_contents>
+        </output>
+        <output name="output_tsv">
+            <assert_contents>
+              <has_text text="9606" />
+              <has_text text="9598" />
+            </assert_contents>
+        </output>
+      </test>
+      <test>
+        <param name="api" value="pept2taxa"/>
+        <param name="fmt" value="fasta"/>
+        <param name="input_fasta" value="peptide.fa"/>
+        <param name="equate_il" value="True"/>
+        <param name="extra" value="False"/>
+        <param name="names" value="False"/>
+        <param name="selected_outputs" value="tsv"/>
+        <output name="output_tsv">
+            <assert_contents>
+              <has_text text="sapiens" />
+              <has_text text="troglodytes" />
+              <has_text text="Gorilla" />
+              <has_text text="Macaca" />
+            </assert_contents>
+        </output>
+      </test>
+      <test>
+        <param name="api" value="pept2lca"/>
+        <param name="fmt" value="tabular"/>
+        <param name="input_tsv" value="tryptic.tsv"/>
+        <param name="column" value="2"/>
+        <param name="extra" value="True"/>
+        <param name="names" value="True"/>
+        <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,unmatched"/>
+        <output name="output_tsv">
+            <assert_contents>
+              <has_text text="3.2.1.17" />
+            </assert_contents>
+        </output>
+        <output name="output_ec_tsv">
+            <assert_contents>
+              <has_text text="3.2.1.17" />
+            </assert_contents>
+        </output>
+        <output name="output_go_tsv">
+            <assert_contents>
+              <has_text text="GO:0006412" />
+            </assert_contents>
+        </output>
+      </test>
+    </tests>
+    <help><![CDATA[
+    **Unipept** 
+
+    Retrieve Uniprot and taxanomic information for trypic peptides.
+    
+    Unipept API documentation - http://unipept.ugent.be/apidocs 
+
+    **Input**
+
+    Input peptides can be retrieved from tabular, fasta, mzid, or pepxml datasets.  
+ 
+    Processing deatils::
+
+        The input peptides are split into typtic peptide fragments in order to match the Unipept records.   
+        Only fragments that are complete tryptic peptides between 5 and 50 animo acid in length will be matched by Unipept.
+        The match to the most specific tryptic fragment is reported.
+
+
+    **Unipept APIs**
+
+    **pept2prot**  - http://unipept.ugent.be/apidocs/pept2prot
+
+    Returns the list of UniProt entries containing a given tryptic peptide. This is the same information as provided on the Protein matches tab when performing a search with the Tryptic Peptide Analysis in the web interface. 
+
+    By default, each object contains the following information fields extracted from the UniProt record::
+
+        peptide: the peptide that matched this record
+        uniprot_id: the UniProt accession number of the matching record
+        taxon_id: the NCBI taxon id of the organism associated with the matching record
+
+    When the extra parameter is set to true, objects contain the following additional fields extracted from the UniProt record::
+
+        taxon_name: the name of the organism associated with the matching UniProt record
+        ec_references: a space separated list of associated EC numbers
+        go_references: a space separated list of associated GO terms
+        refseq_ids: a space separated list of associated RefSeq accession numbers
+        refseq_protein_ids: a space separated list of associated RefSeq protein accession numbers
+        insdc_ids: a space separated list of associated insdc accession numbers
+        insdc_protein_ids: a space separated list of associated insdc protein accession numbers
+
+
+    **pept2taxa**  - http://unipept.ugent.be/apidocs/pept2taxa
+
+    Returns the set of organisms associated with the UniProt entries containing a given tryptic peptide. This is the same information as provided on the Lineage table tab when performing a search with the Tryptic Peptide Analysis in the web interface.
+
+    By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
+
+        peptide: the peptide that matched this record
+        taxon_id: the NCBI taxon id of the organism associated with the matching record
+        taxon_name: the name of the organism associated with the matching record
+        taxon_rank: the taxonomic rank of the organism associated with the matching record
+
+    When the extra parameter is set to true, objects contain additional information about the lineages of the organism extracted from the NCBI taxonomy. The taxon id of each rank in the lineage is specified using the following information fields::
+
+        superkingdom_id
+        kingdom_id
+        subkingdom_id
+        superphylum_id
+        phylum_id
+        subphylum_id
+        superclass_id
+        class_id
+        subclass_id
+        infraclass_id
+        superorder_id
+        order_id
+        suborder_id
+        infraorder_id
+        parvorder_id
+        superfamily_id
+        family_id
+        subfamily_id
+        tribe_id
+        subtribe_id
+        genus_id
+        subgenus_id
+        species_group_id
+        species_subgroup_id
+        species_id
+        subspecies_id
+        varietas_id
+        forma_id
+
+
+    **pept2lca**  - http://unipept.ugent.be/apidocs/pept2lca
+
+    Returns the taxonomic lowest common ancestor for a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
+
+    By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
+
+        peptide: the peptide that matched this record
+        taxon_id: the NCBI taxon id of the organism associated with the matching record
+        taxon_name: the name of the organism associated with the matching record
+        taxon_rank: the taxonomic rank of the organism associated with the matching record
+
+    When the extra parameter is set to true, objects contain additional information about the lineage of the taxonomic lowest common ancestor extracted from the NCBI taxonomy. The taxon id of each rank in the lineage is specified using the following information fields::
+
+        superkingdom_id
+        kingdom_id
+        subkingdom_id
+        superphylum_id
+        phylum_id
+        subphylum_id
+        superclass_id
+        class_id
+        subclass_id
+        infraclass_id
+        superorder_id
+        order_id
+        suborder_id
+        infraorder_id
+        parvorder_id
+        superfamily_id
+        family_id
+        subfamily_id
+        tribe_id
+        subtribe_id
+        genus_id
+        subgenus_id
+        species_group_id
+        species_subgroup_id
+        species_id
+        subspecies_id
+        varietas_id
+        forma_id
+
+    **pept2ec**  - http://unipept.ugent.be/apidocs/pept2ec
+
+    Returns the functional EC-numbers associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
+
+    By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
+
+        peptide: the peptide that matched this record
+        total_protein_count: Total amount of proteins matched with the given peptide
+        ec_number: EC-number associated with the current tryptic peptide.
+        protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
+        name: Optional, name of the EC-number. Included when the extra parameter is set to true.
+
+
+    **pept2go**  - http://unipept.ugent.be/apidocs/pept2go
+
+    Returns the functional GO-terms associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
+
+    By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
+
+        peptide: the peptide that matched this record
+        total_protein_count: Total amount of proteins matched with the given peptide
+        go_term: The GO-term associated with the current tryptic peptide.
+        protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
+        name: Optional, name of the GO-term. Included when the extra parameter is set to true.
+
+
+    **pept2funct**  - http://unipept.ugent.be/apidocs/pept2funct
+
+    Returns the functional EC-numbers and GO-terms associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
+
+    By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
+
+        peptide: the peptide that matched this record
+        total_protein_count: Total amount of proteins matched with the given peptide
+        ec_number: EC-number associated with the current tryptic peptide.
+        protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
+        name: Optional, name of the EC-number. Included when the extra parameter is set to true.
+        go_term: The GO-term associated with the current tryptic peptide.
+        protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
+        name: Optional, name of the GO-term. Included when the extra parameter is set to true.
+
+
+    **Attributions**
+
+    The Unipept metaproteomics analysis pipeline
+    Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1
+    Article first published online: 11 FEB 2015
+    DOI: 10.1002/pmic.201400361
+    http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400361/abstract;jsessionid=BFF1994E4C14DA73D7C907EB208AD710.f04t04
+
+    ]]></help>
+  <citations>
+    <citation type="doi">doi:10.1002/pmic.201400361</citation>
+  </citations>
+
+</tool>