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annotate bamhash.xml @ 1:a19b36f7ff5d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f-dirty
author bgruening
date Thu, 17 Sep 2015 06:21:17 -0400
parents c76494b4ba50
children 27f5da0a6bd9
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c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
bgruening
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1 <tool id="bamhash" name="BamHash" version="1.1">
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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2 <description>Hash BAM and FASTQ files to verify data integrity</description>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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3 <requirements>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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4 <requirement type="package" version="1.1">bamhash</requirement>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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5 </requirements>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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6 <stdio>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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7 <exit_code range="1:" />
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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8 <exit_code range=":-1" />
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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9 <regex match="Error:" />
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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10 <regex match="Exception:" />
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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11 </stdio>
1
a19b36f7ff5d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f-dirty
bgruening
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12 <version_command>bamhash_checksum_fastq --version</version_command>
0
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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13 <command><![CDATA[
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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14 #if $tool.tool_choice=="bam":
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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15 #for $counter, $file in enumerate($tool.input_bam):
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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16 ln -s "${file}" "${counter}.bam" ## 1.bam ... 2.bam
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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17 &&
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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18 #end for
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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19 bamhash_checksum_bam
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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20 $tool.noQuality_bam
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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21 $tool.noPaired_bam
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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22 #for $counter, $filename in enumerate($tool.input_bam):
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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23 "${counter}.bam"
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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24 #end for
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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25 #elif $tool.tool_choice=="fastq":
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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26 #for $counter, $file in enumerate($tool.input_fastq):
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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27 ln -s "${file}" "${counter}.fastq" ## 1.fastq ... 2.fastq
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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28 &&
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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29 #end for
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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30 bamhash_checksum_fastq
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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31 $tool.noQuality_fastq
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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32 $tool.noPaired_fastq
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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33 #for $counter, $filename in enumerate($tool.input_fastq):
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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34 "${counter}.fastq"
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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35 #end for
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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36 #elif $tool.tool_choice=="fasta":
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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37 #for $counter, $file in enumerate($tool.input_fasta):
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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38 ln -s "${file}" "${counter}.fasta" ## 1.fasta ... 2.fasta
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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39 &&
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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40 #end for
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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41 bamhash_checksum_fasta
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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42 #for $counter, $filename in enumerate($tool.input_fasta):
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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43 "${counter}.fasta"
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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44 #end for
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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45 #end if
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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46 $readnames
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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47 > output.txt
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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48 ]]></command>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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49 <inputs>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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50 <conditional name="tool">
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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51 <param name="tool_choice" type="select" label="Choose file type:"
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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52 help="">
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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53 <option value="bam">BAM file(s)</option>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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54 <option value="fastq">FASTQ file(s)</option>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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55 <option value="fasta">FASTA file(s)</option>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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56 </param>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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57 <when value="bam">
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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58 <param name="input_bam" multiple="True" type="data" format="bam" label="Input file - BAM format"/>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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59 <param name="noQuality_bam" type="boolean" checked="false" truevalue="--no-quality"
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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60 falsevalue=""
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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61 label="Ignore read quality?"
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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62 help="Do not use read quality as part of checksum"/>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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63 <param name="noPaired_bam" type="boolean" checked="false" truevalue="--no-paired"
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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64 falsevalue=""
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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65 label="Bam files were not generated with paired-end reads?"/>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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66 </when>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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67 <when value="fasta">
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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68 <param name="input_fasta" multiple="True" type="data" format="fasta" label="Input file - FASTA format"/>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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69 </when>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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70 <when value="fastq">
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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71 <param name="input_fastq" multiple="True" type="data" format="fastq" label="Input file - FASTQ format"/>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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72 <param name="noQuality_fastq" type="boolean" checked="false" truevalue="--no-quality"
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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73 falsevalue=""
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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74 label="Ignore read quality?"
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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75 help="Do not use read quality as part of checksum"/>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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76 <param name="noPaired_fastq" type="boolean" checked="false" truevalue="--no-paired"
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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77 falsevalue=""
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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78 label="List of fastq files are not paired-end reads?"/>
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79 </when>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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80 </conditional>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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81 <param name="readnames" type="boolean" checked="false" truevalue="--no-readnames"
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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82 falsevalue=""
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83 label="Ignore readnames?"
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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84 help="Do not use read names as part of checksum"/>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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85
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86 </inputs>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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87 <outputs>
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88 <data name="output" format="txt" from_work_dir="./output.txt"
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89 label="${tool.name} on ${on_string}">
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90 </data>
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91 </outputs>
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92 <tests>
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93 <test>
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94 <param name="input_bam" value="Example.bam" ftype="bam"/>
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95 <param name="tool_choice" value="bam"/>
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96 <output name="output" file="output1_bam.txt" ftype="txt"/>
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97 </test>
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98 <test>
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99 <param name="input_fasta" value="UnAligSeq24606.fasta" ftype="fasta"/>
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100 <param name="tool_choice" value="fasta"/>
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101 <param name="readnames" value="--no-readnames"/>
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102 <output name="output" file="output2_fasta.txt" ftype="txt"/>
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103 </test>
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104 <test>
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105 <param name="input_fastq" value="1_mismatch.fastq,2_mismatch.fastq" ftype="fastq"/>
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106 <param name="tool_choice" value="fastq"/>
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107 <param name="noQuality" value="--no-quality"/>
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108 <output name="output" file="output3_fastq.txt" ftype="txt"/>
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109 </test>
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110 <test>
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111 <param name="input_fastq" value="1_mismatch.fastq,2_mismatch.fastq" ftype="fastq"/>
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112 <param name="tool_choice" value="fastq"/>
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113 <output name="output" file="output4_fastq.txt" ftype="txt"/>
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114 </test>
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115 </tests>
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116 <help><![CDATA[
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117
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118 **WHAT IT DOES**
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119
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120 Hash BAM and FASTQ files to verify data integrity
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121
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122 For each pair of reads in a BAM or FASTQ file we compute a hash value composed of the readname,
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123 whether it is first or last in pair, sequence and quality value. All the hash values are summed
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124 up so the result is independent of the ordering within the files. The result can be compared to
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125 verify that the pair of FASTQ files contain the same read information as the aligned BAM file.
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126
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127 -----
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128
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129 **BAM**
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130
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131 processes a number of BAM files. BAM files are assumed to contain paired end reads.
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132 If you run with --no-paired it treats all reads as single end and displays a warning if any read is marked as "second in pair" in the BAM file.
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133
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134 -----
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135
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136 **FASTA**
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137
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138 processes a number of FASTA files. All FASTA files are assumed to be single end reads with no quality information.
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139 To compare to a BAM file, run bamhash_checksum_bam --no-paired --no-quality
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140
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141 -----
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142
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143
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144 **FASTQ**
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145
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146 processes a number of FASTQ files. FASTQ files are assumed to contain paired end reads,
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147 such that the first two files contain the first pair of reads, etc. If any of the read names in the two pairs don't match the program exits with failure.
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148
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149
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150 -----
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151
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152
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153 **BamHash** is a Free and Open Source Software, see more details on the BamHash github_ Website.
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154
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155 .. _github: https://github.com/DecodeGenetics/BamHash
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156
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157 ]]></help>
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158 <citations>
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159 </citations>
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160 </tool>