Mercurial > repos > public-health-bioinformatics > micall_lite

annotate micall_lite.xml @ 0:023064145bea draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
author public-health-bioinformatics
date Mon, 06 Jan 2020 19:10:15 -0500
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children bb549c5eaf34
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0
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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1 <tool id="micall_lite" name="micall_lite" version="@TOOL_VERSION@+galaxy0">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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2 <description></description>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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3 <macros>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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4 <import>macros.xml</import>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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5 </macros>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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6 <requirements>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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7 <requirement type="package" version="@TOOL_VERSION@">micall-lite</requirement>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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8 </requirements>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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9 <version_command>echo "@TOOL_VERSION@"</version_command>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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10 <command detect_errors="exit_code">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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11 <![CDATA[
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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12 #if str( $fastq_input.fastq_input_selector ) == "paired":
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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13 #if $fastq_input.reads1.is_of_type("fastq.gz", "fastqsanger.gz"):
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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14 #set unzipped = False
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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15 #set reads1 = $fastq_input.reads1.element_identifier + '_R1.fastq.gz'
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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16 #else if $fastq_input.reads1.is_of_type("fastq", "fastqsanger"):
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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17 #set unzipped = True
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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18 #set reads1 = $fastq_input.reads1.element_identifier + '_R1.fastq'
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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19 #end if
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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20 ln -s '$fastq_input.reads1' '$reads1' &&
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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21 #if $fastq_input.reads2.is_of_type("fastq.gz", "fastqsanger.gz"):
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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22 #set unzipped = False
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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23 #set reads2 = $fastq_input.reads2.element_identifier + '_R2.fastq.gz'
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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24 #else if $fastq_input.reads2.is_of_type("fastq", "fastqsanger"):
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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25 #set unzipped = True
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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26 #set reads2 = $fastq_input.reads2.element_identifier + '_R2.fastq'
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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27 #end if
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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28 ln -s '$fastq_input.reads2' '$reads2' &&
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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29 #else if str( $fastq_input.fastq_input_selector ) == "paired_collection":
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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30 #if $fastq_input.pair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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31 #set unzipped = False
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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32 #set reads1 = $fastq_input.pair.element_identifier + '_R1.fastq.gz'
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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33 #else if $fastq_input.pair.forward.is_of_type("fastq", "fastqsanger"):
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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34 #set unzipped = True
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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35 #set reads1 = $fastq_input.pair.element_identifier + '_R1.fastq'
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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36 #end if
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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37 ln -s '$fastq_input.pair.forward' '$reads1' &&
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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38 #if $fastq_input.pair.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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39 #set unzipped = False
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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40 #set reads2 = $fastq_input.pair.element_identifier + '_R2.fastq.gz'
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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41 #else if $fastq_input.pair.reverse.is_of_type("fastq", "fastqsanger"):
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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42 #set unzipped = True
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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43 #set reads2 = $fastq_input.pair.element_identifier + '_R2.fastq'
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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44 #end if
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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45 ln -s '$fastq_input.pair.reverse' '$reads2' &&
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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46 #end if
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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47
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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48 mkdir 'outdir' &&
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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49 micall
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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50 --threads \${GALAXY_SLOTS:-1}
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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51 #if $unzipped:
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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52 --unzipped
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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53 #end if
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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54 --readlen ${readlen}
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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55 '${reads1}'
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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56 '${reads2}'
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57 --outdir 'outdir'
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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58 ]]>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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59 </command>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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60 <inputs>
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61 <conditional name="fastq_input">
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62 <param name="fastq_input_selector" type="select" label="Paired Reads or Paired Collection" >
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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63 <option selected="true" value="paired">Paired</option>
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64 <option value="paired_collection">Paired Collection</option>
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65 </param>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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66 <when value="paired">
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67 <param format="@INTYPES@" name="reads1" type="data" label="Select first set of reads"/>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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68 <param format="@INTYPES@" name="reads2" type="data" label="Select second set of reads"/>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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69 </when>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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70 <when value="paired_collection">
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71 <param format="@INTYPES@" name="pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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72 </when>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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73 </conditional>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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74 <param name="readlen" type="integer" min="1" value="251" max="600" label="Read Length" help="Read Length" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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75 </inputs>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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76 <outputs>
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77 <data name="align" label="align" format="csv" from_work_dir="outdir/*.align.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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parents:
diff changeset
78 <data name="amino" label="amino" format="csv" from_work_dir="outdir/*.amino.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
79 <data name="conseq" label="conseq" format="csv" from_work_dir="outdir/*.conseq.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
80 <data name="insert" label="insert" format="csv" from_work_dir="outdir/*.insert.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
81 <data name="nuc" label="nuc" format="csv" from_work_dir="outdir/*.nuc.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
82 </outputs>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
83 <tests>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
84 <test>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
85 <conditional name="fastq_input">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
86 <param name="fastq_input_selector" value="paired"/>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
87 <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
88 <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
89 </conditional>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
90 <param name="readlen" value="51" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
91 <output name="align" value="1234A-V3LOOP.align.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
92 <output name="amino" value="1234A-V3LOOP.amino.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
93 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
94 <output name="insert" value="1234A-V3LOOP.insert.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
95 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
96 </test>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
97 <test>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
98 <conditional name="fastq_input">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
99 <param name="fastq_input_selector" value="paired"/>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
100 <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
101 <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
102 </conditional>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
103 <param name="readlen" value="51" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
104 <output name="align" value="1234A-V3LOOP.align.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
105 <output name="amino" value="1234A-V3LOOP.amino.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
106 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
107 <output name="insert" value="1234A-V3LOOP.insert.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
108 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
109 </test>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
110 <test>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
111 <conditional name="fastq_input">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
112 <param name="fastq_input_selector" value="paired_collection" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
113 <param name="pair" >
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
114 <collection type="paired">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
115 <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
116 <element name="reverse" value="1234A-V3LOOP_S1_L001_R2_001.fastq" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
117 </collection>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
118 </param>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
119 </conditional>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
120 <param name="readlen" value="51" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
121 <output name="align" value="1234A-V3LOOP.align.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
122 <output name="amino" value="1234A-V3LOOP.amino.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
123 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
124 <output name="insert" value="1234A-V3LOOP.insert.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
125 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
126 </test>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
127 <test>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
128 <conditional name="fastq_input">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
129 <param name="fastq_input_selector" value="paired_collection" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
130 <param name="pair" >
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
131 <collection type="paired">
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
132 <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
133 <element name="reverse" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
134 </collection>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
135 </param>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
136 </conditional>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
137 <param name="readlen" value="51" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
138 <output name="align" value="1234A-V3LOOP.align.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
139 <output name="amino" value="1234A-V3LOOP.amino.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
140 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
141 <output name="insert" value="1234A-V3LOOP.insert.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
142 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
143 </test>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
144 </tests>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
145 <help><![CDATA[
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
146 ]]></help>
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
147 <expand macro="citations" />
023064145bea "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
parents:
diff changeset
148 </tool>