Mercurial > repos > proteore > filter_keywords_values

comparison filter_kw_val.xml @ 5:1e9911190142 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty
author proteore
date Wed, 14 Mar 2018 10:24:54 -0400
parents 2c1012e0a628
children 6f32c1e12572
comparison
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4:2c1012e0a628 5:1e9911190142
53 <option value="text">Enter keywords (copy/paste)</option> 53 <option value="text">Enter keywords (copy/paste)</option>
54 <option value="file">Choose a file containing keywords</option> 54 <option value="file">Choose a file containing keywords</option>
55 </param> 55 </param>
56 <when value="None" /> 56 <when value="None" />
57 <when value="text" > 57 <when value="text" >
58 <param name="txt" type="text" label="Copy/paste keywords to be removed" help='Keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175' > 58 <param name="txt" type="text" label="Copy/paste keywords to be filtered out" help='Keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175' >
59 <sanitizer> 59 <sanitizer>
60 <valid initial="string.printable"> 60 <valid initial="string.printable">
61 <remove value="&apos;"/> 61 <remove value="&apos;"/>
62 </valid> 62 </valid>
63 <mapping initial="none"> 63 <mapping initial="none">
104 </repeat> 104 </repeat>
105 105
106 </inputs> 106 </inputs>
107 <outputs> 107 <outputs>
108 <data name="output1" format="tabular" label="${tool.name} on ${input1.name}" /> 108 <data name="output1" format="tabular" label="${tool.name} on ${input1.name}" />
109 <data name="trash_file" format="tabular" label="${tool.name} on ${input1.name} - Removed lines" /> 109 <data name="trash_file" format="tabular" label="${tool.name} on ${input1.name} - Filtered lines" />
110 </outputs> 110 </outputs>
111 <tests> 111 <tests>
112 <test> 112 <test>
113 <param name="input1" value="Lacombe_et_al_2017_OK.txt" /> 113 <param name="input1" value="Lacombe_et_al_2017_OK.txt" />
114 <param name="header" value="true" /> 114 <param name="header" value="true" />
123 <output name="output1" file="FKW_Lacombe_et_al_2017_OK.txt" /> 123 <output name="output1" file="FKW_Lacombe_et_al_2017_OK.txt" />
124 <output name="trash_file" file="Trash_FKW_Lacombe_et_al_2017_OK.txt" /> 124 <output name="trash_file" file="Trash_FKW_Lacombe_et_al_2017_OK.txt" />
125 </test> 125 </test>
126 </tests> 126 </tests>
127 <help><![CDATA[ 127 <help><![CDATA[
128 This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output). 128 This tool allows to filter out data according to your specific needs (e.g. contaminants, non-significant values or related to a particular annotation) from a proteomics results file (e.g. MaxQuant or Proline output).
129 129
130 **For each row, if there are more than one protein IDs/protein names/gene names, only the first one will be considered in the output** 130 **For each row, if there are more than one protein IDs/protein names/gene names, only the first one will be considered in the output**
131 131
132 **Filter the file by keywords** 132 **Filter the file by keywords**
133 133
141 141
142 TRYP_PIG 142 TRYP_PIG
143 143
144 ALDOA_RABBIT 144 ALDOA_RABBIT
145 145
146 **The line that contains these keywords will be eliminated from input file.** 146 **The line that contains these keywords will be filtered from input file and provided in a separate file.**
147 147
148 **Keywords search can be applied by performing either exact match or partial one by using the following option** 148 **Keywords search can be applied by performing either exact match or partial one by using the following option**
149 149
150 - If you choose **Yes**, only the fields that contains exactly the same content will be removed. 150 - If you choose **Yes**, only the fields that contains exactly the same content will be filtered.
151 151
152 - If you choose **No**, all the fields containing the keyword will be removed. 152 - If you choose **No**, all the fields containing the keyword will be filtered.
153 153
154 For example: 154 For example:
155 155
156 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed. 156 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is filtered (and not "Kinase").
157 157
158 **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed. 158 **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed.
159 159
160 **Filter the file by values** 160 **Filter the file by values**
161 161
167 167
168 The tool will produce 2 output files. 168 The tool will produce 2 output files.
169 169
170 * A text file containing the resulting filtered input file. 170 * A text file containing the resulting filtered input file.
171 171
172 * A text file containing the rows removed from the input file. 172 * A text file containing the rows that have been filtered from the input file.
173 173
174 ----- 174 -----
175 175
176 .. class:: infomark 176 .. class:: infomark
177 177