Mercurial > repos > iuc > bctools_extract_barcodes

annotate extract_bcs.xml @ 0:8fbf997d64c0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
author iuc
date Tue, 14 Nov 2017 05:50:52 -0500
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children 47262bbf8904
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8fbf997d64c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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1 <tool id="bctools_extract_barcodes" name="Extract barcodes" version="@VERSION@">
8fbf997d64c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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2 <description>according to pattern</description>
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3 <macros>
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4 <import>macros.xml</import>
8fbf997d64c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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5 </macros>
8fbf997d64c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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6 <expand macro="requirements"/>
8fbf997d64c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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7 <command detect_errors="exit_code"><![CDATA[
8fbf997d64c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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8 extract_bcs.py
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9 '$reads'
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10 #if $barcode_pattern and $barcode_pattern is not None:
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11 '$barcode_pattern'
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12 #end if
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13 --bcs '$extracted_barcodes'
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14 > '$reads_cleaned'
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15 ]]></command>
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16 <inputs>
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17 <param name="reads" type="data" format="fastq" label="Barcoded sequences" />
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18 <param name="barcode_pattern" type="text" label="Pattern for extracting barcode nucleotides" help="Starting at 5'-end. X positions will be moved to a separate file, N positions will be kept.">
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19 <sanitizer invalid_char="N">
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20 <valid initial="none">
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21 <add value="X"/>
8fbf997d64c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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22 <add value="N"/>
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23 </valid>
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24 </sanitizer>
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25 </param>
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26 </inputs>
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27 <outputs>
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28 <data name="reads_cleaned" format="fastq"/>
8fbf997d64c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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29 <data name="extracted_barcodes" format="fastq"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="reads" value="reads.fastq"/>
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34 <param name="barcode_pattern" value="XXXNNXXX"/>
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35 <output name="reads_cleaned" file="result_original_head.fastq"/>
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36 <output name="extracted_barcodes" file="extracted_bcs.fastq"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40
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41 bctools - Extract barcodes according to pattern
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42 ===============================================
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43
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44 Exract barcodes from a FASTQ file according to a user-specified pattern and write them to a separate FASTQ file.
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45
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46 ]]></help>
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47 <expand macro="citations"/>
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48 </tool>