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annotate data_manager/novoalign_index_builder.xml @ 0:85fbd52dbb36 draft

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planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
author sanbi-uwc
date Thu, 03 Mar 2016 05:59:41 -0500
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children 4d67344bdea7
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85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
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1 <?xml version="1.0" encoding="utf-8" ?>
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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2 <tool id="novoalign_index_builder" name="NOVO ALIGN index" version="0.0.1">
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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3 <description>Build an index for use by the Novo Align mapping tool</description>
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4 <requirements>
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5 <requirement type="package" version="0.0.1d">novoalign</requirement>
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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6 </requirements>
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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7 <stdio>
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8 <exit_code range=":-1" />
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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9 <exit_code range="1:" />
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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10 </stdio>
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11 <command interpreter="python">
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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12 novoalign_index_builder.py "${out_file}" --data_table_name "novo_index"
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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13 </command>
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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14 <inputs>
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15 <conditional name="reference_source">
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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16 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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17 <option value="url">URL</option>
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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18 <option value="history">History</option>
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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19 <option value="directory">Directory on Server</option>
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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20 </param>
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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21 <when value="url">
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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22 <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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23 </when>
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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24 <when value="history">
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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25 <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" />
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
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26 </when>
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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27 <when value="directory">
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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28 <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" />
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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29 <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to orignal data instead of copying" checked="False" />
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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30 </when>
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31 </conditional>
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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32 <!-- <param type="text" name="sequence_name" value="" label="Name of sequence" />
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33 <param type="text" name="sequence_id" value="" label="ID for sequence" /> -->
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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34 </inputs>
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35 <outputs>
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36 <data name="out_file" format="data_manager_json" />
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="dbkey" value="anoGam1"/>
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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41 <param name="sequence_name" value=""/>
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42 <param name="sequence_id" value=""/>
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43 <param name="reference_source_selector" value="history"/>
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44 <param name="input_fasta" value="phiX174.fasta"/>
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45 <param name="sort_selector" value="as_is"/>
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46 <output name="out_file" file="phiX174_as_anoGam1.data_manager_json"/>
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47 </test>
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48 </tests>
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49 <help>Help!</help>
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50 <citations>
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51 <citation></citation>
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52 </citations>
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53 </tool>