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annotate kma_map.xml @ 0:abcd73320f34 draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/kma/ commit 53a42565eaad1ef0da3e47329dcc93d8841f780e-dirty
author dfornika
date Thu, 03 Oct 2019 01:10:37 -0400
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children 0cea5eb0fa0e
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abcd73320f34 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/kma/ commit 53a42565eaad1ef0da3e47329dcc93d8841f780e-dirty
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1 <tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy0">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">kma</requirement>
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8 </requirements>
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9 <version_command>kma -v</version_command>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
abcd73320f34 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/kma/ commit 53a42565eaad1ef0da3e47329dcc93d8841f780e-dirty
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12 kma
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13 -t \${GALAXY_SLOTS:-1}
abcd73320f34 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/kma/ commit 53a42565eaad1ef0da3e47329dcc93d8841f780e-dirty
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14 -t_db '${kma_index.fields.path}'
abcd73320f34 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/kma/ commit 53a42565eaad1ef0da3e47329dcc93d8841f780e-dirty
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15 #if $single_paired.single_paired_selector == 'yes'
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16 -ipe '${single_paired.forward_input}' '${single_paired.reverse_input}'
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17 #elif $single_paired.single_paired_selector == "collection":
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18 -ipe '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
abcd73320f34 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/kma/ commit 53a42565eaad1ef0da3e47329dcc93d8841f780e-dirty
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19 #else:
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20 -i '${single_paired.input_sequences}'
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21 #end if
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22 -o output
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23 ]]>
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24 </command>
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25 <inputs>
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26 <conditional name="single_paired">
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27 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
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28 <option value="collection">Collection</option>
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29 <option value="yes">Paired</option>
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30 <option selected="True" value="no">Single</option>
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31 </param>
abcd73320f34 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/kma/ commit 53a42565eaad1ef0da3e47329dcc93d8841f780e-dirty
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32 <when value="collection">
abcd73320f34 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/kma/ commit 53a42565eaad1ef0da3e47329dcc93d8841f780e-dirty
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33 <param format="fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
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34 </when>
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35 <when value="yes">
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36 <param format="fastq" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
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37 <param format="fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
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38 </when>
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39 <when value="no">
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40 <param format="fastq" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>
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41 </when>
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42 </conditional>
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43 <param name="kma_index" type="select">
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44 <options from_data_table="kma_index">
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45 <validator type="no_options" message="No KMA index available" />
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46 </options>
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47 </param>
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48 </inputs>
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49 <outputs>
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50 <data name="res" label="result overview" format="tabular" from_work_dir="output.res" />
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51 <data name="aln" label="consensus alignment" format="aln" from_work_dir="output.aln" />
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52 </outputs>
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53 <tests>
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54 </tests>
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55 <help>
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56 <![CDATA[
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57 ]]>
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58 </help>
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59 <expand macro="citations" />
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60 </tool>