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annotate macros.xml @ 7:fcadce4d9a06 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:18:09 -0400
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7
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <macros>
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3 <token name="@WRAPPER_VERSION@">0.14</token>
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4 <xml name="requirements_stdio">
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5 <requirements>
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6 <requirement type="package" version="0.1.19">samtools</requirement>
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7 <yield/>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" />
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11 <exit_code range=":-1" />
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12 <regex match="Error:" />
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13 <regex match="Exception:" />
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14 </stdio>
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15 <version_command>bismark --version</version_command>
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16 </xml>
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17
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18 <xml name="single_paired_conditional">
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19 <!-- Input Parameters -->
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20 <conditional name="singlePaired">
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21 <param name="sPaired" type="select" label="Is this library mate-paired?">
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22 <option value="single">Single-end</option>
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23 <option value="paired">Paired-end</option>
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24 </param>
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25 <when value="single">
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26 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
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27 </when>
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28 <when value="paired">
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29 <repeat name="mate_list" title="Paired End Pairs" min="1">
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30 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." />
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31 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." />
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32 </repeat>
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33 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
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34 <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" />
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35 </when>
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36 </conditional>
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37 </xml>
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38
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39 <xml name="advanced_params">
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40 <param name="seed_len" type="integer" value="28" label="Seed length"
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41 help="The number of bases of the high quality end of the read to which the maximum number of mismatches applies. (--seed-len)" />
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42 <param name="qupto" type="integer" value="0" min="0" label="Only aligns the first N reads or read pairs from the input"
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43 help="Default is 0 and means 'no-limit'. (--qupto)"/>
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44 <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input"
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45 help="(--skip-reads)" />
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46
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47 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
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48 label="Write ambiguous reads to an extra output file"
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49 help="Write all reads which produce more than one valid alignment with the same number of lowest
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50 mismatches or other reads that fail to align uniquely. (--output-suppressed-reads-r/l)" />
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51 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
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52 label="Write all reads that could not be aligned to a file. (--output-unmapped-reads-r/l)" />
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53
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54 <!-- output Options -->
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55 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" />
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56 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" />
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57 <!--end output options -->
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58
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59 </xml>
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60 <xml name="citation">
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61 <citations>
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62 <citation type="doi">10.1093/bioinformatics/btr167</citation>
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63 </citations>
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64 </xml>
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65 </macros>