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1 <tool id="glytools_rename_KCF" name="GAP Rename KCF" version="0.3">
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2 <description>rename the ENTRY tag in KCF file</description>
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3 <requirements>
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4 <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
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5 </requirements>
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6 <command interpreter="python"><![CDATA[ rename_kcf.py -i $input -o $kcfoutput -p $prefix -c $counter]]></command>
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7 <inputs>
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8 <param format="kcf" name="input" type="data" label="KCF source file"/>
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9 <param name="prefix" type="text" value="GLY" optional="false" label="Prefix for renaming ENTRY" help="Type in a prefix for renaming entry"/>
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10 <param name="counter" type="integer" value="0" min="0" max="10000" optional="false" label="Integer start counter for renaming ENTRY"/>
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11 </inputs>
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12 <outputs>
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13 <data format="kcf" name="kcfoutput" label="Renamed KCF $input.name"/>
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14 </outputs>
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15
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16 <citations>
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17 <!-- -->
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18 <citation type="doi">10.1002/0471250953.bi0112s38</citation>
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19 </citations>
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20
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21 <help> <![CDATA[
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22 .. class:: infomark
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23
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24 **What this tool does**
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25
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26 This tool reads KCF glycans and sequentially renames them as GLY{$COUNT}. Why? Sometimes entry names have illegal chars e.g. "-" or sometimes they are linearcode. Which seems great but linearcode is too long and has too many illegals chars in it, meaning that other tools along the pipeline start to fail.
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27
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28 .. class:: infomark
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29
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30 **Input**
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31
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32 *KCF*
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33
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34 .. class:: infomark
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35
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36 **Output**
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37
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38 *KCF*
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39
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40 ]]>
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41 </help>
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42
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43 </tool>
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