diff MetaProSIP.xml @ 0:f0e3cb65a6bd draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MetaProSIP.xml	Wed Mar 01 12:39:28 2017 -0500
@@ -0,0 +1,179 @@
+<?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.-->
+<!--Proposed Tool Section: [Utilities]-->
+<tool id="MetaProSIP" name="MetaProSIP" version="2.1.0">
+  <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="stdio"/>
+  <expand macro="requirements"/>
+  <command>MetaProSIP
+
+#if $param_in_mzML:
+  -in_mzML $param_in_mzML
+#end if
+#if $param_in_fasta:
+  -in_fasta $param_in_fasta
+#end if
+#if $param_out_csv:
+  -out_csv $param_out_csv
+#end if
+#if $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
+#if $param_r_executable:
+  -r_executable $param_r_executable
+#end if
+#if $param_mz_tolerance_ppm:
+  -mz_tolerance_ppm $param_mz_tolerance_ppm
+#end if
+#if $param_rt_tolerance_s:
+  -rt_tolerance_s $param_rt_tolerance_s
+#end if
+#if $param_intensity_threshold:
+  -intensity_threshold $param_intensity_threshold
+#end if
+#if $param_correlation_threshold:
+  -correlation_threshold $param_correlation_threshold
+#end if
+#if $param_xic_threshold:
+  -xic_threshold $param_xic_threshold
+#end if
+#if $param_decomposition_threshold:
+  -decomposition_threshold $param_decomposition_threshold
+#end if
+#if $param_weight_merge_window:
+  -weight_merge_window $param_weight_merge_window
+#end if
+#if $param_plot_extension:
+  -plot_extension $param_plot_extension
+#end if
+#if $param_qc_output_directory:
+  -qc_output_directory     "$param_qc_output_directory"
+#end if
+#if $param_labeling_element:
+  -labeling_element $param_labeling_element
+#end if
+#if $param_use_unassigned_ids:
+  -use_unassigned_ids
+#end if
+#if $param_use_averagine_ids:
+  -use_averagine_ids
+#end if
+#if $param_report_natural_peptides:
+  -report_natural_peptides
+#end if
+#if $param_filter_monoisotopic:
+  -filter_monoisotopic
+#end if
+#if $param_cluster:
+  -cluster
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_min_correlation_distance_to_averagine:
+  -min_correlation_distance_to_averagine $adv_opts.param_min_correlation_distance_to_averagine
+#end if
+    #if $adv_opts.param_pattern_15N_TIC_threshold:
+  -pattern_15N_TIC_threshold $adv_opts.param_pattern_15N_TIC_threshold
+#end if
+    #if $adv_opts.param_pattern_13C_TIC_threshold:
+  -pattern_13C_TIC_threshold $adv_opts.param_pattern_13C_TIC_threshold
+#end if
+    #if $adv_opts.param_pattern_2H_TIC_threshold:
+  -pattern_2H_TIC_threshold $adv_opts.param_pattern_2H_TIC_threshold
+#end if
+    #if $adv_opts.param_pattern_18O_TIC_threshold:
+  -pattern_18O_TIC_threshold $adv_opts.param_pattern_18O_TIC_threshold
+#end if
+    #if $adv_opts.param_heatmap_bins:
+  -heatmap_bins $adv_opts.param_heatmap_bins
+#end if
+    #if $adv_opts.param_observed_peak_fraction:
+  -observed_peak_fraction $adv_opts.param_observed_peak_fraction
+#end if
+    #if $adv_opts.param_min_consecutive_isotopes:
+  -min_consecutive_isotopes $adv_opts.param_min_consecutive_isotopes
+#end if
+    #if $adv_opts.param_score_plot_yaxis_min:
+  -score_plot_yaxis_min $adv_opts.param_score_plot_yaxis_min
+#end if
+    #if $adv_opts.param_collect_method:
+  -collect_method $adv_opts.param_collect_method
+#end if
+    #if $adv_opts.param_lowRIA_correlation_threshold:
+  -lowRIA_correlation_threshold $adv_opts.param_lowRIA_correlation_threshold
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+#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) "/>
+    <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/>
+    <param name="param_r_executable" type="data" format="text" value="R" label="Path to the R executable (default: 'R')" help="(-r_executable) "/>
+    <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>
+    <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/>
+    <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_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>
+      <option value="H">H</option>
+      <option value="O">O</option>
+    </param>
+    <param name="param_use_unassigned_ids" display="radio" type="boolean" truevalue="-use_unassigned_ids" falsevalue="" checked="false" optional="True" label="Include identifications not assigned to a feature in pattern detection" help="(-use_unassigned_ids) "/>
+    <param name="param_use_averagine_ids" display="radio" type="boolean" truevalue="-use_averagine_ids" falsevalue="" checked="false" optional="True" label="Use averagine peptides as model to perform pattern detection on unidentified peptides" help="(-use_averagine_ids) "/>
+    <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) "/>
+    <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) "/>
+      <param name="param_pattern_13C_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_13C_TIC_threshold) "/>
+      <param name="param_pattern_2H_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_2H_TIC_threshold) "/>
+      <param name="param_pattern_18O_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_18O_TIC_threshold) "/>
+      <param name="param_heatmap_bins" type="integer" value="20" label="Number of RIA bins for heat map generation" help="(-heatmap_bins) "/>
+      <param name="param_observed_peak_fraction" type="float" value="0.5" label="Fraction of observed/expected peaks" help="(-observed_peak_fraction) "/>
+      <param name="param_min_consecutive_isotopes" type="integer" value="2" label="Minimum number of consecutive isotopic intensities needed" help="(-min_consecutive_isotopes) "/>
+      <param name="param_score_plot_yaxis_min" type="float" value="0.0" label="The minimum value of the score axis" help="(-score_plot_yaxis_min) Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/>
+      <param name="param_collect_method" display="radio" type="select" optional="False" value="correlation_maximum" label="How RIAs are collected" help="(-collect_method) ">
+        <option value="correlation_maximum" selected="true">correlation_maximum</option>
+        <option value="decomposition_maximum">decomposition_maximum</option>
+      </param>
+      <param name="param_lowRIA_correlation_threshold" type="float" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="(-lowRIA_correlation_threshold) Disable and take correlation_threshold value for negative values"/>
+      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out_csv" format="tabular"/>
+    <data name="param_out_peptide_centric_csv" format="tabular"/>
+  </outputs>
+  <help>Performs proteinSIP on peptide features for elemental flux analysis.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_MetaProSIP.html</help>
+</tool>