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3
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1 <tool id="shear_assemble" name="SHEAR-Assemble" version="0.0.11">
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0
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2 <description>create a personal genome from sdi</description>
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3 <requirements>
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3
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4 <requirement type="package" version="0.2.11">shear</requirement>
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0
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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 interpreter="python">
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10 shear_wrapper.py -j \$SHEAR_JAR_PATH/SHEAR.jar --command assemble
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11 -p $prefix
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12 -s $sdi_file
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13 #if $genomeSource.refGenomeSource == 'indexed':
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14 -f $genomeSource.ref_fastas.fields.path
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15 #else:
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16 -f $genomeSource.ref_fasta
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17 #end if
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18 -o $output_fasta
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19 </command>
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20 <inputs>
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21 <param name="prefix" type="text" value="shear_assemble" label="Prefix for all generated files">
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22 <validator type="regex" message="Prefix should start with a letter and contain only letter, digit, and '_' or '-' characters">[a-zA-Z0-9][_a-zA-Z0-9-]*</validator>
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23 </param>
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24 <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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25 <!-- reference data -->
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26 <conditional name="genomeSource">
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27 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a cached file?">
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28 <option value="indexed">Use a cached reference genome</option>
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29 <option value="history">Use one from the history</option>
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30 </param>
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31 <when value="indexed">
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32 <param name="ref_fastas" type="select" label="Select a reference genome">
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33 <options from_data_table="all_fasta">
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34 <filter type="sort_by" column="2" />
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35 <validator type="no_options" message="No reference fasta files are available" />
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36 </options>
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37 </param>
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38 </when>
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39 <when value="history">
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40 <param name="ref_fasta" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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41 </when>
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42 </conditional>
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43 </inputs>
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44 <stdio>
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45 <exit_code range="1:" level="fatal" description="Error" />
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46 </stdio>
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47 <outputs>
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48 <data format="fasta" name="output_fasta" label="${tool.name} on ${on_string}: ${prefix}.fa" />
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="prefix" value="shear_assembly" />
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53 <param name="sdi_file" value="shear_sv.sdi" ftype="shear.sdi" />
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54 <param name="refGenomeSource" value="history"/>
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55 <param name="ref_fasta" value="syn.fa" ftype="fasta" />
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56 <output name="output_fasta" file="simulated-data.fa"/>
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57 </test>
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58 </tests>
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59 <help>
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60 SHEAR-Assemble takes a reference genome and a *.sdi file from SHEAR-SV to create a new personal genome.
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2
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61
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62 Please cite the following article:
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63
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64 Landman SR, Hwang TH, Silverstein KAT, Li Y, Dehm SM, Steinbach M, and Kumar V. SHEAR: sample heterogeneity estimation and assembly by reference. BMC Genomics 2014, 15:84.
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65
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0
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66 </help>
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67 </tool>
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