Mercurial > repos > iuc > varscan_somatic
annotate varscan_somatic.xml @ 1:31a38ce7e8ae draft
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
author | iuc |
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date | Sun, 15 Jul 2018 09:19:25 -0400 |
parents | 72b8ce355fae |
children | 2fe9ebb98aad |
rev | line source |
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1
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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1 <tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.1"> |
0
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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2 <description>Call germline/somatic variants from tumor-normal pileups</description> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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3 <macros> |
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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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4 <import>macros.xml</import> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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5 </macros> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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6 <expand macro="requirements" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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7 <expand macro="stdio" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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8 <command><![CDATA[ |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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9 varscan somatic |
1
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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10 @INPUT_PILEUPS@ |
0
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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11 --min-coverage ${min_coverage} |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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12 --min-reads2 ${min_reads2} |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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13 --min-avg-qual ${min_avg_qual} |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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14 --min-var-freq ${min_var_freq} |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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15 --min-freq-for-hom ${min_freq_for_hom} |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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16 --normal-purity ${normal_purity} |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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17 --tumor-purity ${tumor_purity} |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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18 --tumor-purity ${tumor_purity} |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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19 --min-coverage-normal ${min_coverage_normal} |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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20 --somatic-p-value ${somatic_p_value} |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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21 --p-value ${p_value} |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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22 #if str($strand_filter) == 'yes': |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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23 --strand-filter 1 |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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24 #end if |
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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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25 |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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26 --output-vcf 1 |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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27 ]]></command> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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28 |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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29 <inputs> |
1
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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30 |
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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31 <expand macro="input_pileups"/> |
0
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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32 |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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33 <expand macro="min_coverage" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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34 <param argument="--min-coverage-normal" name="min_coverage_normal" type="integer" value="8" min="1" max="200" |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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35 label="Minimum read depth from the normal sample" help="Minimum depth at a position to make a call" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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36 <param argument="--min-coverage-tumor" name="min_coverage_tumor" type="integer" value="6" min="1" max="200" |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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37 label="Minimum read depth from the tumor sample" help="Minimum depth at a position to make a call" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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38 <expand macro="min_reads2" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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changeset
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39 <expand macro="min_avg_qual" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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40 <expand macro="min_var_freq" value="0.10" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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41 <expand macro="min_freq_for_hom" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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42 <param argument="--normal-purity" name="normal_purity" type="float" value="1.00" min="0" max="1.00" |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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43 label="Estimated purity (non-tumor content) of normal sample"/> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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44 <param argument="--tumor-purity" name="tumor_purity" type="float" value="1.00" min="0" max="1.00" |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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45 label="Estimated purity (tumor content) of tumor sample"/> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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46 <expand macro="p_value" label="P-value threshold to call a heterozygote" value="0.99"/> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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47 <param argument="--somatic-p-value" name="somatic_p_value" type="float" value="0.05" min="0" max="1" |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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48 label="p-value threshold for calling somatic sites"/> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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49 <expand macro="strand_filter" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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50 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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51 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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52 <data name="output_indel" from_work_dir="galaxy_out.indel.vcf" format="vcf"/> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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53 <data name="output_snp" from_work_dir="galaxy_out.snp.vcf" format="vcf"/> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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54 </outputs> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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55 <tests> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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56 <test> |
1
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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57 <conditional name="pileup"> |
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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58 <param name="pileup_select" value="separated" /> |
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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59 <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" /> |
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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60 <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" /> |
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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61 </conditional> |
0
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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62 <param name="min_coverage" value="2" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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63 <param name="min_coverage_normal" value="2" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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64 <param name="min_coverage_tumor" value="2" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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65 <param name="min_reads2" value="1" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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66 <param name="min_avg_qual" value="5" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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67 <param name="min_var_freq" value="0.01" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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68 <param name="min_freq_for_hom" value="0.75" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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69 <param name="normal_purity" value="0.6" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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70 <param name="tumor_purity" value="0.6" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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71 <param name="p_value" value="0.99" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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72 <output name="output_indel" file="varscan_somatic_indel_result1.vcf" lines_diff="0" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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73 <output name="output_snp" file="varscan_somatic_snp_result1.vcf" lines_diff="0" /> |
72b8ce355fae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
parents:
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changeset
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74 </test> |
1
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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75 <test> |
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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76 <conditional name="pileup"> |
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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77 <param name="pileup_select" value="combined" /> |
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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78 <param name="combined_pileup" value="NT.pileup.gz" /> |
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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79 </conditional> |
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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80 <param name="min_coverage" value="2" /> |
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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81 <param name="min_coverage_normal" value="2" /> |
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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82 <param name="min_coverage_tumor" value="2" /> |
31a38ce7e8ae
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
iuc
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83 <param name="min_reads2" value="1" /> |
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84 <param name="min_avg_qual" value="5" /> |
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85 <param name="min_var_freq" value="0.01" /> |
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86 <param name="min_freq_for_hom" value="0.75" /> |
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87 <param name="normal_purity" value="0.6" /> |
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88 <param name="tumor_purity" value="0.6" /> |
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89 <param name="p_value" value="0.99" /> |
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90 <output name="output_indel" file="varscan_somatic_indel_result2.vcf" lines_diff="0" /> |
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91 <output name="output_snp" file="varscan_somatic_snp_result2.vcf" lines_diff="0" /> |
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92 </test> |
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93 </tests> |
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94 |
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95 <help> |
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96 **VarScan Overview** |
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97 |
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98 VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. |
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99 It calls variants from a mpileup dataset and produces a VCF 4.1. Full documentation is available online_. |
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100 |
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101 This tool calls germline/somatic variants from tumor-normal pileups. |
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102 |
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103 .. _VarScan: http://dkoboldt.github.io/varscan/ |
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104 .. _online: http://dkoboldt.github.io/varscan/using-varscan.html |
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105 |
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106 **Input** |
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107 |
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108 :: |
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109 |
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110 mpileup file - The SAMtools mpileup files for the normal and tumor tissue |
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111 |
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112 |
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113 **Output** |
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114 |
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115 VarScan produces a VCF 4.1 dataset as output. |
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116 |
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117 |
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118 </help> |
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119 <expand macro="citations" /> |
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120 </tool> |