# HG changeset patch
# User galaxyp
# Date 1446742486 18000
# Node ID d239e445e2e6afd77cad931de63a30fe41c73027
# Parent  16cb7537c1a2b7ba059cb3268e3ffa4a6818f847
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 8eadb7632f9240724b853adc997558779bfe7219-dirty

diff -r 16cb7537c1a2 -r d239e445e2e6 idpqonvert.xml
--- a/idpqonvert.xml	Tue Sep 15 17:50:14 2015 -0400
+++ b/idpqonvert.xml	Thu Nov 05 11:54:46 2015 -0500
@@ -19,7 +19,7 @@
 <![CDATA[
         #set $db_name = $ProteinDatabase.display_name.replace(".fasta", "") + ".fasta"
         #set $input_name = $input.display_name
-        #set $output_name = $input_name.split(".")[0] + ".idpDB"
+        #set $output_name = $input_name.replace(".pep.xml", "").replace(".pepXML", "").replace(".mzid", "") + ".idpDB"
         ln -s '$input' '${input_name}' &&
         ln -s '$ProteinDatabase' '${db_name}' &&
 
@@ -69,17 +69,17 @@
         <param name="input" type="data" format="mzid,raw_pepxml" label="Input mzIdentML/pepXML file(s)" />
         <param argument="-ProteinDatabase" format="fasta" type="data" label="Protein Database" help="The FASTA protein database to map peptides against. Only peptides from target proteins will be mapped; decoy peptides will be stored as-is in the idpDB." />
         <param argument="-DecoyPrefix" type="text" label="Decoy Prefix" help="The prefix to look for on protein accessions to determine whether it is a target or decoy." />
-        <param argument="-MaxFDR" type="float" label="Max FDR" value="0.05" help="PSMs with a greater FDR than this will be excluded from the filtered data set, but remain in the file." />
+        <param argument="-MaxFDR" type="float" label="Max FDR" min="0.0000001" value="0.05" help="PSMs with a greater FDR than this will be excluded from the filtered data set, but remain in the file." />
         <section name="advanced_options" title="Advanced Options">
-            <param argument="-MaxImportFDR" type="float" label="Max Import FDR" value="0.25" help="PSMs with a greater FDR than this will be completely excluded from the idpDB." />
-            <param argument="-MaxResultRank" type="integer" label="Max Result Rank" value="2" />
-            <param argument="-MaxTrainingRank" type="integer" label="Max Training Rank" value="1" />
+            <param argument="-MaxImportFDR" type="float" label="Max Import FDR" min="0.1" value="0.25" help="PSMs with a greater FDR than this will be completely excluded from the idpDB." />
+            <param argument="-MaxResultRank" type="integer" label="Max Result Rank" min="1" value="2" />
+            <param argument="-MaxTrainingRank" type="integer" label="Max Training Rank" min="1" value="1" />
             <param argument="-RerankMatches" type="boolean" label="Rerank Matches" checked="false" truevalue="true" falsevalue="false" />
             <param argument="-Gamma" type="float" label="Gamma" value="5" />
             <param argument="-Nu" type="float" label="Nu" value="-0.5" />
-            <param argument="-TruePositiveThreshold" type="float" label="True Positive Threshold" value="0.01" />
-            <param argument="-PolynomialDegree" type="integer" label="Polynomial Degree" value="3" />
-            <param argument="-MinPartitionSize" type="integer" label="Minimum Partition Size" value="10" />
+            <param argument="-TruePositiveThreshold" type="float" label="True Positive Threshold" min="0.0000001" value="0.01" />
+            <param argument="-PolynomialDegree" type="integer" label="Polynomial Degree" min="1" value="3" />
+            <param argument="-MinPartitionSize" type="integer" label="Minimum Partition Size" min="10" value="10" />
             <param argument="-SVMType" label="SVM Type" type="select">
                 <option value="CSVC" selected="true">CSVC</option>
                 <option value="NuSVC">Nu SCV</option>
@@ -120,53 +120,53 @@
         </section>
         <section name="scoring" title="Custom Score Settings">
             <section name="myrimatch_mvh" title="Myrimatch (mvh) Score/Weight" expanded="False">
-                <param name="myrimatch_mvh_weight" label="Myrimatch (mvh) Weight" type="float" value="1" />
+                <param name="myrimatch_mvh_weight" label="Myrimatch (mvh) Weight" type="float" min="-1" max="1" value="1" />
                 <param name="myrimatch_mvh_type" label="Myrimatch (mvh) Normalization" type="select"><expand macro="normalizationOptions" /></param>
             </section>
             <section name="xcorr" title="Non-Sequest (xcorr) Score/Weight" expanded="False">
-                <param name="xcorr_weight" label="XCorr Weight" type="float" value="1" />
+                <param name="xcorr_weight" label="XCorr Weight" type="float" min="-1" max="1" value="1" />
                 <param name="xcorr_type" label="XCorr Normalization" type="select"><expand macro="normalizationOptions" /></param>
             </section>
             <section name="sequest_xcorr" title="Sequest (xcorr) Score/Weight" expanded="False">
-                <param name="sequest_xcorr_weight" label="Sequest (xcorr) Weight" type="float" value="1" />
+                <param name="sequest_xcorr_weight" label="Sequest (xcorr) Weight" type="float" min="-1" max="1" value="1" />
                 <param name="sequest_xcorr_type" label="Sequest (xcorr) Normalization" type="select"><expand macro="normalizationOptions" /></param>
             </section>
             <section name="sequest_deltacn" title="Sequest (deltacn) Score/Weight" expanded="False">
-                <param name="sequest_deltacn_weight" label="Sequest (deltacn) Weight" type="float" value="1" />
+                <param name="sequest_deltacn_weight" label="Sequest (deltacn) Weight" type="float" min="-1" max="1" value="1" />
                 <param name="sequest_deltacn_type" label="Sequest (deltacn) Normalization" type="select"><expand macro="normalizationOptions" /></param>
             </section>
             <section name="mascot_score" title="Mascot (score) Score/Weight" expanded="False">
-                <param name="mascot_score_weight" label="Mascot Score Weight" type="float" value="1" />
+                <param name="mascot_score_weight" label="Mascot Score Weight" type="float" min="-1" max="1" value="1" />
                 <param name="mascot_score_type" label="Mascot Score Normalization" type="select"><expand macro="normalizationOptions" /></param>
             </section>
             <section name="xtandem_expect" title="X! Tandem (expect) Score/Weight" expanded="False">
-                <param name="xtandem_expect_weight" label="X! Tandem (expectation) Weight" type="float" value="-1" />
+                <param name="xtandem_expect_weight" label="X! Tandem (expectation) Weight" type="float" min="-1" max="1" value="-1" />
                 <param name="xtandem_expect_type" label="X! Tandem (expectation) Normalization" type="select"><expand macro="normalizationOptions" /></param>
             </section>
             <section name="xtandem_hyperscore" title="X! Tandem (hyperscore) Score/Weight" expanded="False">
-                <param name="xtandem_hyperscore_weight" label="X! Tandem (hyperscore) Weight" type="float" value="1" />
+                <param name="xtandem_hyperscore_weight" label="X! Tandem (hyperscore) Weight" type="float" min="-1" max="1" value="1" />
                 <param name="xtandem_hyperscore_type" label="X! Tandem (hyperscore)Normalization" type="select"><expand macro="normalizationOptions" /></param>
             </section>
             <section name="ms-gf_specevalue" title="MS-GF+ (specevalue) Score/Weight" expanded="False">
-                <param name="ms-gf_specevalue_weight" label="MS-GF+ (specevalue) Weight" type="float" value="-1" />
+                <param name="ms-gf_specevalue_weight" label="MS-GF+ (specevalue) Weight" type="float" min="-1" max="1" value="-1" />
                 <param name="ms-gf_specevalue_type" label="MS-GF+ (specevalue) Normalization" type="select"><expand macro="normalizationOptions" /></param>
             </section>
             <section name="comet_xcorr" title="Comet (xcorr) Score/Weight" expanded="False">
-                <param name="comet_xcorr_weight" label="Comet (xcorr) Weight" type="float" value="1" />
+                <param name="comet_xcorr_weight" label="Comet (xcorr) Weight" type="float" min="-1" max="1" value="1" />
                 <param name="comet_xcorr_type" label="Comet (xcorr) Normalization" type="select"><expand macro="normalizationOptions" /></param>
             </section>
             <section name="comet_deltacn" title="Comet (deltacn) Score/Weight" expanded="False">
-                <param name="comet_deltacn_weight" label="Comet (deltacn) Weight" type="float" value="1" />
+                <param name="comet_deltacn_weight" label="Comet (deltacn) Weight" type="float" min="-1" max="1" value="1" />
                 <param name="comet_deltacn_type" label="Comet (deltacn) Normalization" type="select"><expand macro="normalizationOptions" /></param>
             </section>
             <section name="comet_expect" title="Comet (expect) Score/Weight" expanded="False">
-                <param name="comet_expect_weight" label="Comet (expect) Weight" type="float" value="-1" />
+                <param name="comet_expect_weight" label="Comet (expect) Weight" type="float" min="-1" max="1" value="-1" />
                 <param name="comet_expect_type" label="Comet (expect) Normalization" type="select"><expand macro="normalizationOptions" /></param>
             </section>
             <repeat name="extra_score" title="Extra Search Engine Score/Weight">
                 <param name="extra_score_name" label="Name" type="text" help="For scores in the PSI-MS controlled vocabulary, this field must match the name for that score; for other scores, the UserParam name or pepXML name will suffice." value="SearchEngineName" />
                 <param name="extra_score_normalization" label="Normalization Method" type="select"><expand macro="normalizationOptions" /></param>
-                <param name="extra_score_weight" label="Weight" type="float" help="Negative weights indicate that a lower score is better (e.g. expectation value, p-value)." value="1" />
+                <param name="extra_score_weight" label="Weight" type="float" help="Negative weights indicate that a lower score is better (e.g. expectation value, p-value)." min="-1" max="1" value="1" />
             </repeat>
         </section>
     </inputs>