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1 <tool id="shear_assemble" name="SHEAR-Assemble" version="0.0.1">
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2 <description>create a personal genome from sdi</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.2">shear</requirement>
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5 </requirements>
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6 <!--
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7 <version_command></version_command>
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8 -->
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9 <command>java -jar \$SHEAR_JAR_PATH/SHEAR.jar assemble -s $sdi_file
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10 #if $genomeSource.refGenomeSource == 'indexed':
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11 -f $genomeSource.ref_fastas.fields.path
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12 #else:
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13 -f $genomeSource.ref_fasta
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14 #end if
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15 -o $output_fasta
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16 </command>
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17 <inputs>
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18 <param name="sdi_file" type="data" format="shear.sdi" label="SDI file produced by SHEAR's 'sv' command containing the SVs to use to create the new genomic sequence."/>
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19 <!-- reference data -->
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20 <conditional name="genomeSource">
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21 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a cached file?">
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22 <option value="indexed">Use a cached reference genome</option>
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23 <option value="history">Use one from the history</option>
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24 </param>
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25 <when value="indexed">
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26 <param name="ref_fastas" type="select" label="Select a reference genome">
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27 <options from_data_table="all_fasta">
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28 <filter type="sort_by" column="2" />
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29 <validator type="no_options" message="No reference fasta files are available" />
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30 </options>
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31 </param>
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32 </when>
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33 <when value="history">
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34 <param name="ref_fasta" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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35 </when>
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36 </conditional>
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37 </inputs>
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38 <stdio>
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39 <exit_code range="1:" level="fatal" description="Error" />
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40 </stdio>
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41 <outputs>
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42 <data format="fasta" name="output_fasta" label="${tool.name} on ${on_string}: personal genome" />
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="sdi_file" ftype="shear.sdi" value="shear_sv.sdi"/>
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47 <param name="refGenomeSource" value="history"/>
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48 <param name="ref_fasta" ftype="fasta" value="syn.fa"/>
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49 <output name="output_fasta" file="simulated-data.fa"/>
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50 </test>
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51 </tests>
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52 <help>
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53 SHEAR-Assemble takes a reference genome and a *.sdi file from SHEAR-SV to create a new personal genome.
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54 </help>
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55 </tool>
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