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annotate kma_map.xml @ 1:0cea5eb0fa0e draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/kma/ commit e5a95750f732cec753a8c2d8dbca0f63e50205f8-dirty
author dfornika
date Fri, 04 Oct 2019 15:13:01 -0400
parents abcd73320f34
children 1c1dba36c061
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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 $single_paired.single_paired_selector == 'yes'
abcd73320f34 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/kma/ commit 53a42565eaad1ef0da3e47329dcc93d8841f780e-dirty
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16 -ipe '${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}'
abcd73320f34 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/kma/ commit 53a42565eaad1ef0da3e47329dcc93d8841f780e-dirty
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21 #end if
1
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22 -o output &&
0cea5eb0fa0e planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/kma/ commit e5a95750f732cec753a8c2d8dbca0f63e50205f8-dirty
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23 gunzip output.frag.gz
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24 ]]>
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25 </command>
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26 <inputs>
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27 <conditional name="single_paired">
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28 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
abcd73320f34 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/kma/ commit 53a42565eaad1ef0da3e47329dcc93d8841f780e-dirty
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29 <option value="collection">Collection</option>
abcd73320f34 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/kma/ commit 53a42565eaad1ef0da3e47329dcc93d8841f780e-dirty
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30 <option value="yes">Paired</option>
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31 <option selected="True" value="no">Single</option>
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32 </param>
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33 <when value="collection">
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34 <param format="fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
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35 </when>
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36 <when value="yes">
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37 <param format="fastq" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
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38 <param format="fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
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39 </when>
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40 <when value="no">
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41 <param format="fastq" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>
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42 </when>
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43 </conditional>
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44 <param name="kma_index" type="select">
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45 <options from_data_table="kma_index">
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46 <validator type="no_options" message="No KMA index available" />
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47 </options>
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48 </param>
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49 </inputs>
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50 <outputs>
1
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51 <data name="result_overview" label="Result overview" format="tabular" from_work_dir="output.res" />
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52 <data name="consensus_alignment" label="Consensus alignment" format="text" from_work_dir="output.aln" />
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53 <data name="consensus_sequences" label="Consensus sequences" format="fasta" from_work_dir="output.aln" />
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54 <data name="read_mapping" label="Read mapping info" format="tabular" from_work_dir="output.frag" />
0
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55 </outputs>
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56 <tests>
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57 </tests>
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58 <help>
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59 <![CDATA[
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60 ]]>
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61 </help>
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62 <expand macro="citations" />
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63 </tool>