Mercurial > repos > jjohnson > seq2hla
annotate seq2hla.xml @ 1:6ecaa71a5aa3 draft default tip
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit 31729242dd250fc1b89dcdfb74d138450b9ca896
author | jjohnson |
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date | Tue, 01 Oct 2019 10:22:56 -0400 |
parents | 262d5334c786 |
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6ecaa71a5aa3
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit 31729242dd250fc1b89dcdfb74d138450b9ca896
jjohnson
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1 <tool id="seq2hla" name="seq2HLA" version="2.2.0"> |
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262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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2 <description>HLA genotype and expression from RNA-seq</description> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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3 <requirements> |
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6ecaa71a5aa3
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit 31729242dd250fc1b89dcdfb74d138450b9ca896
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4 <requirement type="package" version="2.2">seq2hla</requirement> |
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262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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5 </requirements> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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6 <stdio> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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7 <exit_code range="1:" /> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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8 </stdio> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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9 <command><![CDATA[ |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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10 seq2HLA --runName="$run_name" -1 "$fastq_input1" -2 "$fastq_input2" |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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11 #if str($trim) != '': |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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12 --trim3=$trim |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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13 #end if |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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14 -p \${GALAXY_SLOTS:-1} >> "$seq2hla_log" |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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15 && cp -p "${run_name}-ClassI.HLAgenotype2digits" "${c1_genotype2digits}" |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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16 && cp -p "${run_name}-ClassI.HLAgenotype4digits" "${c1_genotype4digits}" |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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17 && echo "#Locus_RPKM" | cat - "${run_name}-ClassI.expression" | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > "${c1_expression}" |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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18 && cp -p "${run_name}-ClassII.HLAgenotype4digits" "${c2_genotype4digits}" |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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19 && echo "#Locus_RPKM" | cat - "${run_name}-ClassII.expression" | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > "${c2_expression}" |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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20 && cp -p "${run_name}.ambiguity" "${ambiguity}" |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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21 ]]></command> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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22 <inputs> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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23 <param name="run_name" type="text" value="sample1" label="Name prefix for this analysis"> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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24 <validator type="regex" message="Use letters,digits,_.-">^[A-Za-z0-9_\-+.]+$</validator> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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25 </param> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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26 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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27 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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28 <param name="trim" type="integer" value="" min="0" optional="true" label="Trim bases from 3 prime" |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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29 help="trim this many bases from the low-quality end of each read" /> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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30 </inputs> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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31 <outputs> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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32 <data format="txt" name="seq2hla_log" label="${tool.name} on ${on_string}: ${run_name} logfile"/> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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33 <data format="tabular" name="c1_genotype2digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype2digits"/> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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34 <data format="tabular" name="c1_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype4digits"/> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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35 <data format="tabular" name="c2_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassII.HLAgenotype4digits"/> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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36 <data format="tabular" name="c1_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassI.expression"/> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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37 <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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38 <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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39 <data format="txt" name="ambiguity" label="${tool.name} on ${on_string}: ${run_name}.ambiguity"/> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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40 </outputs> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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41 <tests> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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42 <test> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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43 <param name="run_name" value="test"/> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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44 <param name="fastq_input1" ftype="fastqsanger" value="reads1.fastq"/> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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45 <param name="fastq_input2" ftype="fastqsanger" value="reads2.fastq"/> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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46 <output name="c1_genotype4digits"> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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47 <assert_contents> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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48 <has_text text="A*24:02" /> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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49 </assert_contents> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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50 </output> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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51 </test> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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52 </tests> |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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53 <help><![CDATA[ |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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54 **seq2HLA** *HLA typing from RNA-Seq sequence reads* |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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55 |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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56 Release: 2.2 |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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57 |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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58 seq2HLA_ is an in-silico method, written in python and R, which takes standard RNA-Seq sequence reads in fastq format |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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59 as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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60 a p-value for each call, and the expression of each class |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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61 |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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62 **Inputs** |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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63 |
262d5334c786
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64 Paired read fastq files with illumina style IDs. |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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65 |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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66 |
262d5334c786
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67 **Outputs** |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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68 |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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69 1. <prefix>-ClassI.HLAgenotype2digits => 2 digit result of Class I |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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70 2. <prefix>-ClassII.HLAgenotype2digits => 2 digit result of Class II |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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71 3. <prefix>-ClassI.HLAgenotype4digits => 4 digit result of Class I |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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72 4. <prefix>-ClassII.HLAgenotype4digits => 4 digit result of Class II |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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73 5. <prefix>.ambiguity => reports typing ambuigities (more than one solution for an allele possible) |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
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74 6. <prefix>-ClassI.expression => expression of Class I alleles |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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75 7. <prefix>-ClassII.expression => expression of Class II alleles |
262d5334c786
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
jjohnson
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76 |
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77 |
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78 ClassI.HLAgenotype4digits |
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79 |
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80 ======= ======== =========== ======== ============ |
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81 #Locus Allele 1 Confidence Allele 2 Confidence |
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82 ======= ======== =========== ======== ============ |
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83 A A*03:01 0.000510333 A*02:01' 0.0005975604 |
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84 B B*50:01 0.001271273 B*58:02 3.52561e-05 |
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85 C C*04:01 0.06362723 C*06:02 0.04725865 |
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86 ======= ======== =========== ======== ============ |
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87 |
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88 |
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89 ClassI.expression |
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90 |
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91 ======= ====== |
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92 #Locus RPKM |
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93 ======= ====== |
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94 A 89.59 |
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95 B 139.66 |
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96 C 184.42 |
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97 ======= ====== |
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98 |
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99 |
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100 .. _seq2HLA: https://bitbucket.org/sebastian_boegel/seq2hla |
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101 |
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102 ]]></help> |
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103 <citations> |
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104 <citation type="doi">10.1186/gm403</citation> |
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105 </citations> |
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106 </tool> |