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annotate macros.xml @ 1:a12ce5668966 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
author iuc
date Thu, 11 Jun 2015 13:50:36 -0400
parents b98d6fffd00b
children 7a12314c5b64
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b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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1 <macros>
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2 <token name="@WRAPPER_VERSION@">2014.11.03.0</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="2014.11.03">art</requirement>
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7 <yield/>
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8 </requirements>
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9 </xml>
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10
0
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11 <xml name="stdio">
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12 <stdio>
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13 <!-- Anything other than zero is an error -->
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14 <exit_code range="1:" />
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15 <exit_code range=":-1" />
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16 <!-- In case the return code has not been set propery check stderr too -->
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17 <regex match="Error:" />
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18 <regex match="Exception:" />
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19 </stdio>
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20 </xml>
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21 <xml name="aln">
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22 <param type="boolean" label="output ALN alignment file (-a)" name="aln"
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23 truevalue="-a" falsevalue="" />
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24 </xml>
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25 <xml name="sam">
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26 <param type="boolean" label="output SAM alignment file (-s)" name="sam"
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27 truevalue="-s" falsevalue="" />
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28 </xml>
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29
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30 <xml name="rndSeed">
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31 <param label="specify a fixed, random seed for the simulation"
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32 help="Use -1 to request a random seed (-r)" name="rndSeed"
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33 type="integer" value="-1" optional="true" />
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34 </xml>
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35
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36 <xml name="citation">
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37 <citations>
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38 <citation type="doi">10.1093/bioinformatics/btr708</citation>
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39 </citations>
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40 </xml>
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41
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42 <xml name="amplicon">
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43 <conditional name="amplicon">
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44 <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" />
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45 <when value="amplicon_true">
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46 <param label="number of reads per amplicon (for 5'end amplicon sequencing)" name="reads_per_amplicon" type="integer" value="0"/>
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47 </when>
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48 <when value="amplicon_false">
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49 </when>
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50 </conditional>
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51 </xml>
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52
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53 <xml name="amplicon_pair">
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54 <conditional name="amplicon">
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55 <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" />
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56 <when value="amplicon_true">
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57 <param label="number of read pairs per amplicon (for two-end amplicon sequencing)" name="read_pairs_per_amplicon" type="integer" value="0"/>
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58 </when>
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59 <when value="amplicon_false">
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60 </when>
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61 </conditional>
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62 </xml>
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63
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64 <xml name="frag_len_sd">
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65 <param label="the average DNA fragment size"
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66 name="fragment_size" type="integer" value="200" minimum="101" />
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67 <param label="the standard deviation of the DNA fragment size"
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68 name="fragment_sd" type="integer" value="0"/>
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69 </xml>
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70 </macros>