comparison pepnovo_adapter.xml @ 2:cf0d72c7b482 draft

Update.
author galaxyp
date Fri, 10 May 2013 17:31:05 -0400
parents ba86fd127f5a
children
comparison
equal deleted inserted replaced
1:5c65f8116244 2:cf0d72c7b482
1 <tool id="pepnovo_adapter" version="0.1.0" name="PepNovo (OpenMS)"> 1 <tool id="pepnovo_adapter" version="0.1.0" name="PepNovo (OpenMS)">
2 <description> 2 <description>
3
4 </description> 3 </description>
5 <requirements> 4 <macros>
6 <requirement type="package">openms</requirement> 5 <import>macros.xml</import>
6 </macros>
7 <expnad macro="stdio" />
8 <expand macro="requires">
7 <requirement type="package">pepnovo</requirement> 9 <requirement type="package">pepnovo</requirement>
8 </requirements> 10 </expand>
9 <command interpreter="python"> 11 <command interpreter="python">
10 openms_wrapper.py 12 openms_wrapper.py
11 #if $input_block.do_clean 13 #if $input_block.do_clean
12 --executable 'FileConverter' --config $inputConfig 14 --executable 'FileConverter' --config $inputConfig
13 #end if 15 #end if
20 #else 22 #else
21 in=${input_block.input1} 23 in=${input_block.input1}
22 #end if 24 #end if
23 out=${out} 25 out=${out}
24 model_directory=@PEPNOVO_MODELS_PATH@ 26 model_directory=@PEPNOVO_MODELS_PATH@
25 pepnovo_executable=@PEPNOVO_EXECUTABLE_PATH@ 27 pepnovo_executable=@WHICH(PepNovo)@
26 temp_data_directory=. 28 temp_data_directory=.
27 model=${model} 29 model=${model}
28 digest=${digest} 30 digest=${digest}
29 #if $corrections != "none" 31 num_solutions=${num_solutions}
32 #if str($corrections) != "none"
30 correct_pm=true 33 correct_pm=true
31 #end if 34 #end if
32 #if $corrections == "mass" 35 #if str($corrections) == "mass"
33 use_spectrum_charge=true 36 use_spectrum_charge=true
34 #end if 37 #end if
35 #if $corrections == "mz" 38 #if str($corrections) == "mz"
36 use_spectrum_mz=true 39 use_spectrum_mz=true
37 #end if 40 #end if
38 $quality_filter 41 $quality_filter
39 #if $override_pm.do_override 42 #if $override_pm.do_override
40 pm_tolerance=${override_pm.percursor_tolerance} 43 pm_tolerance=${override_pm.percursor_tolerance}
41 #end if 44 #end if
42 #if $override_fragment.do_override 45 #if $override_fragment.do_override
43 fragment_tolerance=${override_fragment.fragment_tolerance} 46 fragment_tolerance=${override_fragment.fragment_tolerance}
47 #end if
48 #set $fixed_mods_str=",".join([str($fixed_mod.fixed_mod) for $fixed_mod in $fixed_mods])
49 #if $fixed_mods_str
50 fixed_modifications=$fixed_mods_str
51 #end if
52 #set $variable_mods_str=",".join([str($variable_mod.variable_mod) for $variable_mod in $variable_mods])
53 #if $variable_mods_str
54 variable_modifications=$variable_mods_str
44 #end if 55 #end if
45 </configfile> 56 </configfile>
46 <configfile name="inputConfig">[simple_options] 57 <configfile name="inputConfig">[simple_options]
47 in=${input_block.input1} 58 in=${input_block.input1}
48 in_type=${input_block.input1.ext} 59 in_type=${input_block.input1.ext}
50 out_type=mzXML 61 out_type=mzXML
51 </configfile> 62 </configfile>
52 </configfiles> 63 </configfiles>
53 <inputs> 64 <inputs>
54 <conditional name="input_block"> 65 <conditional name="input_block">
55 <param name="do_clean" type="boolean" label="Process input peak list" description="The version of PepNovo used by this tool takes only mzXML files and even then fails to parse many valid such files. Enabling this option will run the input peak list (mzXML or otherwise) through the OpenMS FileConverter application to hopefully produce an mzXML file suiteable for PepNovo." /> 66 <param name="do_clean" type="boolean" label="Process input peak list" description="The version of PepNovo used by this tool takes only mzXML files and even then fails to parse many valid such files. Enabling this option will run the input peak list (mzXML or otherwise) through the OpenMS FileConverter application to hopefully produce an mzXML file suitable for PepNovo." />
56 <when value="true"> 67 <when value="true">
57 <param name="input1" type="data" format="mzxml,mzml,mgf,ms2" label="Input peak list" /> 68 <param name="input1" type="data" format="mzxml,mzml,mgf,ms2" label="Input peak list" />
58 </when> 69 </when>
59 <when value="false"> 70 <when value="false">
60 <param name="input1" type="data" format="mzxml" label="Input peak list" /> 71 <param name="input1" type="data" format="mzxml" label="Input peak list" />
74 <option value="none">None.</option> 85 <option value="none">None.</option>
75 <option value="both">Find optimal precursor m/z and charge values.</option> 86 <option value="both">Find optimal precursor m/z and charge values.</option>
76 <option value="mz">Find optimal precursor m/z values.</option> 87 <option value="mz">Find optimal precursor m/z values.</option>
77 <option value="charge">Find optimal charge values.</option> 88 <option value="charge">Find optimal charge values.</option>
78 </param> 89 </param>
90 <repeat name="fixed_mods" title="Fixed Modification">
91 <param name="fixed_mod" type="select" label="Fixed Modification">
92 <options from_file="openms_mods.loc">
93 <column name="name" index="0" />
94 <column name="value" index="0" />
95 </options>
96 </param>
97 </repeat>
98 <repeat name="variable_mods" title="Variable Modification">
99 <param name="variable_mod" type="select" label="Variable Modification">
100 <options from_file="openms_mods.loc">
101 <column name="name" index="0"/>
102 <column name="value" index="0" />
103 </options>
104 </param>
105 </repeat>
79 <param name="quality_filter" type="boolean" checked="true" label="Filter low quality spectra" truevalue="no_quality_filter=true" falsevalue=""/> 106 <param name="quality_filter" type="boolean" checked="true" label="Filter low quality spectra" truevalue="no_quality_filter=true" falsevalue=""/>
80 <conditional name="override_pm"> 107 <conditional name="override_pm">
81 <param name="do_override" type="boolean" label="Override model's percursor mass tolerance" /> 108 <param name="do_override" type="boolean" label="Override model's percursor mass tolerance" />
82 <when value="true"> 109 <when value="true">
83 <param name="percursor_tolerance" type="float" label="Precursor mass tolerance (Daltons)" help="Must between 0 and 5.0. Set to -1.0 to use model default." value="-1.0"> 110 <param name="percursor_tolerance" type="float" label="Precursor mass tolerance (Daltons)" help="Must between 0 and 5.0. Set to -1.0 to use model default." value="-1.0">
95 </param> 122 </param>
96 </when> 123 </when>
97 <when value="false"> 124 <when value="false">
98 </when> 125 </when>
99 </conditional> 126 </conditional>
127 <param name="num_solutions" type="integer" label="Number of Solutions" value="20">
128 <validator type="in_range" message="1 &lt;= Number of Solutions &lt;= 2000" min="1" max="2000"/>
129 </param>
100 </inputs> 130 </inputs>
101 <outputs> 131 <outputs>
102 <data format="idxml" name="out" /> 132 <data format="idxml" name="out" />
103 </outputs> 133 </outputs>
104 <help> 134 <help>