# HG changeset patch
# User jjohnson
# Date 1594137388 14400
# Node ID aa52f0eadc85ba6243dac0e353d501b8158d1c3d
# Parent  174886084dc5b0954c629eacf9e62aa34d04e89f
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"

diff -r 174886084dc5 -r aa52f0eadc85 encyclopedia_quantify.xml
--- a/encyclopedia_quantify.xml	Thu Jul 02 11:07:46 2020 -0400
+++ b/encyclopedia_quantify.xml	Tue Jul 07 11:56:28 2020 -0400
@@ -4,7 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command detect_errors="exit_code"><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         @CMD_IMPORTS@
         @LINK_SCAN_INPUTS@
         @LINK_FASTA_INPUT@
@@ -25,6 +25,7 @@
         @MODIFICATION_OPTIONS@
         @SEARCH_OPTIONS@ | tee -a search2lib.log
         ; done && 
+        for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done &&
         EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport
         @SCAN_INPUTS@
         @FASTA_INPUT@
@@ -32,6 +33,7 @@
         @LIB_INPUT@
         -a $a
         -o chromatogram_library.elib
+        && ls -l ./*.* inputs/*
         | tee -a search2lib.log
     ]]></command>
     <inputs>
@@ -47,6 +49,10 @@
             <option value="features" selected="true">concatenated_features.txt</option>
             <option value="results" selected="true">concatenated_results.txt</option>
             <option value="decoy" selected="false">concatenated_decoy.txt</option>
+            <!--
+            <option value="rt_plots" selected="false">Retention Time Plots</option>
+            <option value="rt_tables" selected="false">Retention Time Tables</option>
+            -->
             <option value="peptides" selected="true">peptides.txt (requires align between files)</option>
             <option value="proteins" selected="true">proteins.txt (requires align between files)</option>
         </param>
@@ -76,13 +82,23 @@
                 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
             </actions>
         </data>
-        <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.peptides.txt">
+        <!--
+        <collection name="rt_plots" type="list" label="${tool.name} - ${on_string}: Retention Time Plots">
+            <filter>l and 'rt_plots' in select_outputs</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" directory="inputs"/>
+        </collection>
+        <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables">
+            <filter>l and 'rt_tables' in select_outputs</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+\.rt_fit\.txt)" ext="tabular" directory="inputs"/>
+        </collection>
+        -->
+        <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.elib.peptides.txt">
             <filter>a and 'peptides' in select_outputs</filter>
             <actions>
                 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" />
             </actions>
         </data>
-        <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.proteins.txt">
+        <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.elib.proteins.txt">
             <filter>a and 'proteins' in select_outputs</filter>
             <actions>
                 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" />
diff -r 174886084dc5 -r aa52f0eadc85 macros.xml
--- a/macros.xml	Thu Jul 02 11:07:46 2020 -0400
+++ b/macros.xml	Tue Jul 07 11:56:28 2020 -0400
@@ -31,14 +31,12 @@
     #end if
 #end def
 #def clean($name1)
-    ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i[.](fa|fasta|imzml|mzml)$)','', $re.sub('.*/','', $name1.rstrip('.gz'))))
-    ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('.*/','', $name1.rstrip('.gz')))
-    #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
+    #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
     #return $name_clean
 #end def
 #def ln_name($ds) 
     #set $ext = ''
-    #if $ds.is_of_type('mzml')
+    #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml')
         #set $ext = ".mzML"
     #else if $ds.is_of_type('elib')
         #set $ext = ".elib"