Mercurial > repos > iuc > optitype
annotate optitype.xml @ 0:fd974c5df8bc draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
author | iuc |
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date | Wed, 17 Feb 2021 08:10:24 +0000 |
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0
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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1 <tool id="optitype" name="OptiType" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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2 <description>HLA genotyping predictions from NGS data</description> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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3 <macros> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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4 <token name="@TOOL_VERSION@">1.3.5</token> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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5 <token name="@VERSION_SUFFIX@">0</token> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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6 </macros> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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7 <requirements> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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8 <requirement type="package" version="@TOOL_VERSION@">optitype</requirement> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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9 </requirements> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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10 <command detect_errors="aggressive"> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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11 <![CDATA[ |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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12 export MPLCONFIGDIR=\$TEMP && |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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13 #set $fastqs = [] |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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14 #if str( $fastq_input.fastq_input_selector ) == "paired": |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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15 ln -s '${fastq_input.fastq_input1}' reads_1.fastq |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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16 && ln -s '${fastq_input.fastq_input2}' reads_2.fastq |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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17 #set $fastqs = ['reads_1.fastq','reads_2.fastq'] |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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18 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection": |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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19 ln -s '${fastq_input.fastq_input1.forward}' reads_1.fastq |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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20 && ln -s '${fastq_input.fastq_input1.reverse}' reads_2.fastq |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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21 #set $fastqs = ['reads_1.fastq','reads_2.fastq'] |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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22 #elif str( $fastq_input.fastq_input_selector ) == "single": |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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23 ln -s '${fastq_input.fastq_input1}' reads.fastq |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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24 #set $fastqs = ['reads.fastq'] |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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25 #end if |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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26 && RAZERS3=`which razers3` |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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27 && sed "s#path_to_razers3#\$RAZERS3#" '$optitype_config' | sed "s/threads=16/threads=\${GALAXY_SLOTS}/" > config.ini |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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28 #set $input_fq = ' '.join($fastqs) |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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29 && OptiTypePipeline.py |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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30 $read_type --input ${' '.join($fastqs)} |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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31 #if str($beta) != '': |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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32 --beta $beta |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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33 #end if |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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34 #if str($enumerations) != '': |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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35 --enumerate $enumerations |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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36 #end if |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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37 --config "`pwd`/config.ini" |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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38 --outdir outdir |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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39 && cp outdir/*/*_coverage_plot.pdf '$coverage_plot' |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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40 && cp outdir/*/*_result.tsv '$result' |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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41 ]]> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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42 </command> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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43 <configfiles> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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44 <configfile name="optitype_config"><![CDATA[ |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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45 [mapping] |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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46 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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47 # Absolute path to RazerS3 binary, and number of threads to use for mapping |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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48 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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49 razers3=path_to_razers3 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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50 threads=16 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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51 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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52 [ilp] |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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53 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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54 # A Pyomo-supported ILP solver. The solver must be globally accessible in the |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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55 # environment OptiType is run, so make sure to include it in PATH. |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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56 # Note: this is NOT a path to the solver binary, but a keyword argument for |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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57 # Pyomo. Examples: glpk, cplex, cbc. |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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58 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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59 solver=$solver |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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60 threads=1 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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61 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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62 [behavior] |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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63 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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64 # tempdir=/path/to/tempdir # we may enable this setting later. Not used now. |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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65 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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66 # Delete intermediate bam files produced by RazerS3 after OptiType finished |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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67 # loading them. If you plan to re-analyze your samples with different settings |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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68 # disabling this option can be a time-saver, as you'll be able to pass the bam |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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69 # files to OptiType directly as input and spare the expensive read mapping |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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70 # step. |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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71 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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72 deletebam=true |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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73 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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74 # In paired-end mode one might want to use reads with just one mapped end (e.g., |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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75 # the other end falls outside the reference region). This setting allows the |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
parents:
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76 # user to keep them with an optionally reduced weight. A value of 0 means they |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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77 # are discarded for typing, 0.2 means single reads are "worth" 20% of paired |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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78 # reads, and a value of 1 means they are treated as valuable as properly mapped |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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79 # read pairs. Note: unpaired reads will be reported on the result coverage plots |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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80 # for completeness, regardless of this setting. |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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81 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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82 unpaired_weight=$unpaired_weight |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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83 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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84 # We call a read pair discordant if its two ends best-map to two disjoint sets |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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85 # of alleles. Such reads can be either omitted or either of their ends treated |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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86 # as unpaired hits. Note: discordant read pairs are reported on the coverage |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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87 # plots as unpaired reads, regardless of this setting. |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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88 |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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89 use_discordant=$use_discordant |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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90 ]]></configfile> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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91 </configfiles> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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92 <inputs> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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93 <conditional name="fastq_input"> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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94 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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95 <option value="paired">Paired</option> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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96 <option value="single">Single</option> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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97 <option value="paired_collection">Paired Collection</option> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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98 </param> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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99 <when value="paired"> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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100 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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101 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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102 </when> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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103 <when value="single"> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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104 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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105 </when> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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106 <when value="paired_collection"> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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107 <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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108 </when> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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109 </conditional> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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110 <param name="read_type" type="select" label="Nucleotide Type" help=""> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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111 <option value="--rna">RNA</option> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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112 <option value="--dna">DNA</option> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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113 </param> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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114 <param name="beta" type="float" value="" min="0.0" max="0.1" optional="true" label="homozygosity beta" help="The beta value for for homozygosity detection (Leave blank for default: 0.009)"/> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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115 <param name="enumerations" type="integer" value="" min="1" max="5" optional="true" label="Enumerations" help="The number of enumerations (Leave blank for default: 1)"/> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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116 <param name="solver" type="select" label="ILP solver" help=""> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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117 <option value="glpk">glpk</option> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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118 <!-- Not currently in OptiType conda package |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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119 <option value="cbc">cbc</option> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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120 <option value="cplex">cplex</option> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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121 --> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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122 </param> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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123 <param name="unpaired_weight" type="float" value="0" min="0.0" max="1.0" label="unpaired_weight"> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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124 <help><![CDATA[ |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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125 In paired-end mode one might want to use reads with just one mapped end (e.g., |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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126 the other end falls outside the reference region). This setting allows the |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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127 user to keep them with an optionally reduced weight. A value of 0 means they |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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128 are discarded for typing, 0.2 means single reads are "worth" 20% of paired |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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129 reads, and a value of 1 means they are treated as valuable as properly mapped |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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130 read pairs. Note: unpaired reads will be reported on the result coverage plots |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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131 for completeness, regardless of this setting. ]]> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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132 </help> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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133 </param> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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134 <param name="use_discordant" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use_discordant"> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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135 <help><![CDATA[ |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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136 We call a read pair discordant if its two ends best-map to two disjoint sets |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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137 of alleles. Such reads can be either omitted or either of their ends treated |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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138 as unpaired hits. Note: discordant read pairs are reported on the coverage |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
iuc
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139 plots as unpaired reads, regardless of this setting. ]]> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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140 </help> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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141 </param> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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142 </inputs> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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143 <outputs> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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144 <data name="coverage_plot" format="pdf" label="${tool.name} on ${on_string} coverage_plot.pdf"/> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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145 <data name="result" format="tabular" label="${tool.name} on ${on_string} result.tsv"> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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146 <actions> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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147 <action name="column_names" type="metadata" default="Solution,A1,A2,B1,B2,C1,C2,Reads,Objective"/> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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148 </actions> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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149 </data> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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150 </outputs> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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151 <tests> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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152 <test> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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153 <conditional name="fastq_input"> |
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154 <param name="fastq_input_selector" value="paired"/> |
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155 <param name="fastq_input1" ftype="fastqsanger" value="rna/CRC_81_N_1_fished.fastq"/> |
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156 <param name="fastq_input2" ftype="fastqsanger" value="rna/CRC_81_N_2_fished.fastq"/> |
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157 </conditional> |
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158 <param name="read_type" value="--rna"/> |
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159 <param name="solver" value="glpk"/> |
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160 <output name="result"> |
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161 <assert_contents> |
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162 <has_text_matching expression="0\tA\*31:01\tA\*68:01\tB\*40:01\tB\*51:01\tC\*03:04\tC\*15:02\t13\d+.\d+\t12\d+.\d+"/> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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163 </assert_contents> |
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164 </output> |
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165 </test> |
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166 <test> |
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167 <conditional name="fastq_input"> |
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168 <param name="fastq_input_selector" value="paired"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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169 <param name="fastq_input1" ftype="fastqsanger" value="exome/NA11995_SRR766010_1_fished.fastq"/> |
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170 <param name="fastq_input2" ftype="fastqsanger" value="exome/NA11995_SRR766010_2_fished.fastq"/> |
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171 </conditional> |
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172 <param name="read_type" value="--dna"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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173 <param name="solver" value="glpk"/> |
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174 <param name="enumerations" value="2"/> |
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175 <param name="unpaired_weight" value="0.2"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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176 <output name="result"> |
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177 <assert_contents> |
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178 <has_text_matching expression="0\tA\*01:01\tA\*01:01\tB\*08:01\tB\*57:01\tC\*06:02\tC\*07:01\t3\d+.\d+\t3\d+.\d+"/> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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179 <has_text_matching expression="1\tA\*01:01\tA\*01:01\tB\*08:01\tB\*08:01\tC\*06:02\tC\*07:01\t3\d+.\d+\t3\d+.\d+"/> |
fd974c5df8bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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180 </assert_contents> |
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181 </output> |
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182 </test> |
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183 </tests> |
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184 <help> |
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185 <![CDATA[ |
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186 **OptiType** |
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187 ============ |
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188 |
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189 OptiType_ is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles. |
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190 |
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191 **INPUTS** |
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192 |
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193 RNA or DNA sequences in fastq format. |
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194 |
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195 **OUTPUTS** |
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196 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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197 result.tsv A TAB-separated file of HLA genotyping predictions: |
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198 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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199 :: |
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200 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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201 A1 A2 B1 B2 C1 C2 Reads Objective |
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202 0 A*31:01 A*68:01 B*40:01 B*51:01 C*15:02 C*03:04 132 128.43599999999998 |
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203 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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204 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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205 coverage_plot.pdf Plots of coverage of HLA genotyping predictions |
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206 |
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207 .. _OptiType: https://github.com/FRED-2/OptiType |
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208 ]]> |
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209 </help> |
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210 <citations> |
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211 <citation type="doi">10.1093/bioinformatics/btu548</citation> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 commit bb5ff6e9d2a643bd8931e8a8912bda72af0b5489"
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212 </citations> |
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213 </tool> |