diff MetaProSIP.xml @ 13:3a2985428366 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

--- a/MetaProSIP.xml	Mon Feb 12 08:37:45 2018 -0500
+++ b/MetaProSIP.xml	Wed May 15 05:13:44 2019 -0400
@@ -1,18 +1,19 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="MetaProSIP" name="MetaProSIP" version="2.2.0.1">
+<tool id="MetaProSIP" name="MetaProSIP" version="2.3.2">
   <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
   <macros>
     <token name="@EXECUTABLE@">MetaProSIP</token>
     <import>macros.xml</import>
   </macros>
-  <expand macro="references"/>
+  <expand macro="requirements">
+    <requirement type="package" version="3.4.1">r-base</requirement>
+    <requirement type="package" version="3.0.1">r-gplots</requirement>
+  </expand>
   <expand macro="stdio"/>
-  <expand macro="requirements">
-      <requirement type="package" version="3.3.1">r-base</requirement>
-  </expand>
-  <command>MetaProSIP
+  <command detect_errors="aggressive"><![CDATA[
+MetaProSIP
 
 #if $param_in_mzML:
   -in_mzML $param_in_mzML
@@ -24,14 +25,11 @@
   -out_csv $param_out_csv
 #end if
 #if $param_out_peptide_centric_csv:
-  -out_peptide_centric_csv $param_out_peptide_centric_csv
+  -out_peptide_centric_csv param_out_peptide_centric_csv
 #end if
 #if $param_in_featureXML:
   -in_featureXML $param_in_featureXML
 #end if
-
--r_executable 'R'
-
 #if $param_mz_tolerance_ppm:
   -mz_tolerance_ppm $param_mz_tolerance_ppm
 #end if
@@ -61,9 +59,7 @@
     $param_plot_extension
   #end if
 #end if
-#if $param_qc_output_directory:
-  -qc_output_directory     "$param_qc_output_directory"
-#end if
+-qc_output_directory images
 #if $param_labeling_element:
   -labeling_element
   #if " " in str($param_labeling_element):
@@ -130,7 +126,29 @@
   -force
 #end if
 #end if
-</command>
+-threads "\${GALAXY_SLOTS:-1}"
+
+## - add comment char to first line, 
+## - remove leading/trailing spaces in fields
+## - remove empty line(s) 
+## - remove 'file://' and get basename of filenames in the table
+## - add empty fields as '0' (MetaproSIP output has varying number of output columns, ie it omits the last columns if there are no values)
+&& cat param_out_peptide_centric_csv | 
+	sed '1 s/^/#/' | 
+	sed 's/\t /\t/g; s/ \t/\t/g; s/ /_/g' | 
+	grep -v "^$" | 
+	sed "s/\tfile:\/\//\t/g; s/\t\/[^\t]\+\//\t/g; s/\.$param_plot_extension//g" | 
+	awk -v FS='\t' 'BEGIN{line=0}{if(line==0){ncol=NF; print $0}else{printf("%s",$0); for(i=0; i<ncol-NF; i++){printf("\t0")}printf("\n")}line+=1}' > "$param_out_peptide_centric_csv"
+
+## get html file (should be only one [?])
+
+#if $param_collection or $param_plot_extension == 'pdf'
+	&& rm -f images/*\.html
+#else
+	&& mv images/*\.html '${html_file}'
+	&& mv images/ '${html_file.files_path}'
+#end if
+ ]]></command>
   <inputs>
     <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/>
     <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/>
@@ -140,21 +158,13 @@
     <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
     <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/>
     <param name="param_xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="(-xic_threshold) If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
-    <param name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R^2 of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/>
+    <param name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R² of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/>
     <param name="param_weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help="(-weight_merge_window) "/>
     <param name="param_plot_extension" display="radio" type="select" optional="False" value="png" label="Extension used for plots (png|svg|pdf)" help="(-plot_extension) ">
       <option value="png" selected="true">png</option>
       <option value="svg">svg</option>
       <option value="pdf">pdf</option>
     </param>
-    <param name="param_qc_output_directory" type="text" size="30" label="Output directory for the quality report" help="(-qc_output_directory) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
-    </param>
     <param name="param_labeling_element" display="radio" type="select" optional="False" value="C" label="Which element (single letter code) is labeled" help="(-labeling_element) ">
       <option value="C" selected="true">C</option>
       <option value="N">N</option>
@@ -166,6 +176,7 @@
     <param name="param_report_natural_peptides" display="radio" type="boolean" truevalue="-report_natural_peptides" falsevalue="" checked="false" optional="True" label="Whether purely natural peptides are reported in the quality report" help="(-report_natural_peptides) "/>
     <param name="param_filter_monoisotopic" display="radio" type="boolean" truevalue="-filter_monoisotopic" falsevalue="" checked="false" optional="True" label="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" help="(-filter_monoisotopic) "/>
     <param name="param_cluster" display="radio" type="boolean" truevalue="-cluster" falsevalue="" checked="false" optional="True" label="Perform grouping" help="(-cluster) "/>
+    <param name="param_collection" type="boolean" checked="true" label="output images as collection" help="if enabled images are written to a collection amd to a webpage otherwise (pdf is always written to a collection)"/>
     <expand macro="advanced_options">
       <param name="param_min_correlation_distance_to_averagine" type="float" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="(-min_correlation_distance_to_averagine) Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1"/>
       <param name="param_pattern_15N_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_15N_TIC_threshold) "/>
@@ -185,11 +196,30 @@
     </expand>
   </inputs>
   <outputs>
-    <data name="param_out_csv" format="tabular"/>
-    <data name="param_out_peptide_centric_csv" format="tabular"/>
+    <data name="param_out_csv" format="tabular" label="${tool.name} on ${on_string}: tabular"/>
+    <data name="param_out_peptide_centric_csv" format="tabular" label="${tool.name} on ${on_string}: peptide centric tabular"/>
+    <data format="html" name="html_file" label="${tool.name} on ${on_string}: Webpage">
+      <filter>not param_collection and (param_plot_extension == 'png' or param_plot_extension == 'svg')</filter>
+    </data>
+    <collection name="images" type="list" label="${tool.name} on ${on_string}: images">
+      <filter>param_collection or param_plot_extension == 'pdf'</filter>
+      <discover_datasets pattern="__name_and_ext__" directory="images" />
+    </collection>
   </outputs>
+  <tests>
+    <test>
+      <param name="param_in_mzML" value="MetaProSIP_1_input.mzML" ftype="mzml"/>
+      <param name="param_in_fasta" value="MetaProSIP_1_input.fasta" ftype="fasta"/>
+      <param name="param_in_featureXML" value="MetaProSIP_1_input.featureXML" ftype="featurexml"/>
+      <output name="param_out_csv" file="MetaProSIP_1_output_1.csv"/>
+      <output name="param_out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv"  compare="sim_size" lines_diff="2"/>
+    </test>
+  </tests>
   <help>Performs proteinSIP on peptide features for elemental flux analysis.
 
+	  ** Galaxy specific notes **
 
-For more information, visit http://www.openms.de/comp/metaprosip/</help>
+	  The peptide centric tabular data set generated by the tool is not rendered properly by Galaxy, because it has more than 50 columns. You might extract columns of interst. 
+  </help>
+<expand macro="references"/>
 </tool>