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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
author iuc
date Mon, 14 Jan 2019 15:17:56 -0500
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fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
iuc
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1 <?xml version="1.0"?>
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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2 <tool id="shorah_amplicon" version="@VERSION@+galaxy0" name="Reconstruct haplotypes">
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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3 <description>with ShoRAH in amplicon mode</description>
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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4 <macros>
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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5 <token name="@VERSION@">1.1.3</token>
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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6 </macros>
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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7 <requirements>
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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8 <requirement type="package" version="@VERSION@">shorah</requirement>
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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9 </requirements>
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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10 <command detect_errors="exit_code">
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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11 <![CDATA[
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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12 ln -s '$bam' input.bam &&
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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13 ln -s '$fasta' input.fa &&
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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14 amplian.py
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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15 --bam input.bam
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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16 --fasta input.fa
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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17 #if str($region):
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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18 --region '$region'
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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19 #end if
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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20 $diversity
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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21 --min_overlap $min_overlap
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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22 --alpha $alpha
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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23 --maxcov $maxcov
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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24 --sigma $sigma &&
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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25 sed -i.bak 's/,/\t/g' SNVs_0.010000_final.csv
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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26
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27 ]]>
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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28 </command>
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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29 <inputs>
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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30 <param argument="--bam" type="data" format="bam" label="Aligned reads in .bam format" />
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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31 <param argument="--fasta" type="data" format="fasta" label="Reference genome in fasta format" />
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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32 <param argument="--region" type="text" value="" optional="true" label="Limit to a specific region" help="e.g. 'ch3:1000-1300'" />
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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33 <param argument="--diversity" type="boolean" truevalue="--diversity" falsevalue="" label="Run on the highest entropy region" />
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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34 <param argument="--min_overlap" type="float" value="0.95" min="0" max="1" optional="true" label="Fraction of read overlap to be included" />
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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35 <param argument="--alpha" type="float" value="0.5" optional="true" label="Alpha in dpm sampling" />
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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36 <param argument="--maxcov" type="integer" value="50000" optional="true" label="Approximate max coverage allowed" />
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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37 <param argument="--sigma" type="float" value="0.01" optional="true" label="Sigma value to use when calling SNVs" />
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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38 <param name="log_output" type="boolean" truevalue="log" falsevalue="" label="Include the log in the history" />
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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39 </inputs>
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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40 <outputs>
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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41 <data name="haplotypes" format="tabular" from_work_dir="SNVs_0.010000_final.csv" label="${tool.name} on ${on_string}: Haplotypes" />
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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42 <data name="log" format="txt" from_work_dir="SNV.txt" label="${tool.name} on ${on_string}: Log">
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43 <filter>log_output</filter>
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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44 </data>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="bam" ftype="bam" value="shorah-amplicon-in1.bam" />
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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49 <param name="fasta" ftype="fasta" value="shorah-amplicon-in1.fa" />
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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50 <param name="min_overlap" value="0.95" />
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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51 <param name="log_output" value="log" />
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52 <output name="haplotypes" file="shorah-amplicon-out1.tsv" compare="re_match" />
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53 <output name="log" file="shorah-amplicon-out1.txt" compare="re_match" />
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54 </test>
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55 </tests>
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56 <help>
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57 <![CDATA[
fc46049f6c27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah commit e302de4f94384825ead064acc33b33fc95c081d9
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58 ShoRAH is an open source project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools are written in different programming languages and provide error correction, haplotype reconstruction and estimation of the frequency of the different genetic variants present in a mixed sample.
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59 ]]>
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60 </help>
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61 <citations>
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62 <citation type="doi">10.1186/1471-2105-12-119</citation>
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63 </citations>
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64 </tool>