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annotate searchtolib.xml @ 1:8f2555d3687f draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 7567c513925da467828c9f0dc1746a16b4adb062
author galaxyp
date Fri, 20 Sep 2019 11:01:22 -0400
parents 39618cb4669f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
galaxyp
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1 <tool id="searchtolib" name="SearchToLib" version="@VERSION@.0">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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2 <description>PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data</description>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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3 <macros>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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4 <import>macros.xml</import>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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5 </macros>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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8 @CMD_IMPORTS@
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9 @LINK_SCAN_INPUTS@
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10 @LINK_FASTA_INPUT@
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11 @LINK_TARGET_FASTA@
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12 for SCAN_FILE in `ls -1 inputs/*`; do
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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13 echo "\$SCAN_FILE" &&
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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14 EncyclopeDIA -Djava.awt.headless=true -Xmx12g $search_app
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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15 -i \$SCAN_FILE
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16 @FASTA_INPUT@
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17 @TARGET_FASTA@
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18 @COMMON_OPTIONS@
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19 @MASS_LIBRARY_TOLERANCE@
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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20 @PERCOLATOR_OPTIONS@
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21 @PEAK_OPTIONS@
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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22 @WINDOW_OPTIONS@
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23 @MODIFICATION_OPTIONS@
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24 @SEARCH_OPTIONS@ | tee -a search2lib.log
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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25 ; done &&
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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26 EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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27 $search_app
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28 @SCAN_INPUTS@
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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29 @FASTA_INPUT@
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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30 @TARGET_FASTA@
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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31 @COMMON_OPTIONS@
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32 @MASS_LIBRARY_TOLERANCE@
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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33 @PERCOLATOR_OPTIONS@
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34 @PEAK_OPTIONS@
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35 @WINDOW_OPTIONS@
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36 @MODIFICATION_OPTIONS@
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37 @SEARCH_OPTIONS@
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38 -o gxpedia
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39 | tee -a search2lib.log
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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40 ]]></command>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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41 <inputs>
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42 <expand macro="scan_inputs"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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43 <expand macro="fasta_input"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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44 <expand macro="target_fasta"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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45 <param name="search_app" type="select" label="Search with">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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46 <option value="" selected="true">EncyclopeDIA</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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47 <option value="-pecan">Pecan</option>
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48 <option value="-xcordia">XCorDIA</option>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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49 </param>
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50 <expand macro="common_options"/>
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51 <expand macro="mass_library_tolerance"/>
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52 <expand macro="percolator_options"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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53 <expand macro="peak_options"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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54 <expand macro="window_options"/>
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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55 <expand macro="modification_options"/>
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56 <expand macro="search_options"/>
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57 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
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58 <option value="log" selected="true">log</option>
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59 <option value="elib" selected="true">elib</option>
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60 <option value="features" selected="true">concatenated_features.txt</option>
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61 <option value="results" selected="true">concatenated_results.txt</option>
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62 <option value="decoy" selected="true">concatenated_decoy.txt</option>
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63 <option value="peptides" selected="true">peptides.txt</option>
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64 <option value="proteins" selected="true">proteins.txt</option>
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65 </param>
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66 </inputs>
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67 <outputs>
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68 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="search2lib.log">
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69 <filter>'log' in select_outputs</filter>
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70 </data>
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71 <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="gxpedia">
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72 <filter>'elib' in select_outputs</filter>
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73 </data>
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74 <data name="features" format="tabular" label="${tool.name} ${on_string} concatenated_features.txt" from_work_dir="inputs/gxpedia_concatenated_features.txt">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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75 <filter>'features' in select_outputs</filter>
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76 <actions>
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77 <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" />
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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78 </actions>
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79 </data>
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80 <data name="results" format="tabular" label="${tool.name} ${on_string} concatenated_results.txt" from_work_dir="inputs/gxpedia_concatenated_results.txt">
39618cb4669f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
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81 <filter>'results' in select_outputs</filter>
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82 <actions>
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83 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
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84 </actions>
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85 </data>
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86 <data name="decoy" format="tabular" label="${tool.name} ${on_string} concatenated_decoy.txt" from_work_dir="inputs/gxpedia_concatenated_decoy.txt">
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87 <filter>'decoy' in select_outputs</filter>
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88 <actions>
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89 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
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90 </actions>
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91 </data>
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92 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="gxpedia.peptides.txt">
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93 <filter>'peptides' in select_outputs</filter>
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94 <actions>
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95 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" />
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96 </actions>
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97 </data>
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98 <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="gxpedia.proteins.txt">
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99 <filter>'proteins' in select_outputs</filter>
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100 <actions>
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101 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" />
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102 </actions>
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103 </data>
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104 </outputs>
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105 <help><![CDATA[
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106 SearchToLIB uses EncyclopeDIA, Walnut (Pecan), or XCorDIA to create an DIA Elib for EncyclopeDIA DIA search
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107 Walnut is a FASTA database search engine for DIA data that uses PECAN-style scoring.
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108 You should prefix your arguments with a high memory setting, e.g. "-Xmx8g" for 8gb
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109
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110 Required Parameters:
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111 -i input .DIA or .MZML file
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112 -f background FASTA file
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113
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114 Other Parameters:
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115 -t target FASTA file (default: background FASTA file)
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116 -tp true/false target FASTA file contains peptides (default: false)
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117 -o output report file (default: [input file].pecan.txt)
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118 -acquisition (default: overlapping dia)
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119 -addDecoysToBackground (default: false)
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120 -alpha (default: 1.8)
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121 -beta (default: 0.4)
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122 -dontRunDecoys (default: false)
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123 -enzyme (default: trypsin)
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124 -filterPeaklists (default: false)
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125 -fixed (default: C=57.0214635)
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126 -foffset (default: 0)
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127 -frag (default: YONLY)
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128 -ftol (default: 10)
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129 -ftolunits (default: ppm)
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130 -maxCharge (default: 3)
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131 -maxLength (default: 100)
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132 -maxMissedCleavage (default: 1)
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133 -minCharge (default: 2)
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134 -minEluteTime (default: 12)
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135 -minIntensity (default: -1.0)
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136 -minLength (default: 5)
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137 -minNumOfQuantitativePeaks (default: 3)
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138 -minQuantitativeIonNumber (default: 3)
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139 -numberOfQuantitativePeaks (default: 5)
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140 -numberOfReportedPeaks (default: 1)
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141 -numberOfThreadsUsed (default: 12)
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142 -percolatorProteinThreshold (default: 0.01)
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143 -percolatorThreshold (default: 0.01)
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144 -percolatorVersionNumber (default: 3)
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145 -poffset (default: 0)
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146 -precursorIsolationMargin (default: 0)
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147 -precursorWindowSize (default: -1)
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148 -ptol (default: 10)
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149 -ptolunits (default: ppm)
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150 -requireVariableMods (default: false)
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151 -variable (default: -)
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152
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153 ]]></help>
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154 <expand macro="citations" />
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155 </tool>