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annotate bamhash.xml @ 4:37a9f9f502a2 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 95a9df153f7396894dc7ba2eceb8660fc728b87d
author bgruening
date Tue, 04 Oct 2016 22:58:08 -0400
parents 27f5da0a6bd9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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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
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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">
3
27f5da0a6bd9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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58 <param name="input_bam" multiple="True" type="data" format="bam" label="Input file in BAM format"/>
0
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?"
3
27f5da0a6bd9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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62 help="Do not use read quality as part of checksum. (--no-quality)"/>
0
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=""
3
27f5da0a6bd9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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65 label="Bam files were not generated with paired-end reads?"
27f5da0a6bd9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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66 help="(--no-paired)" />
0
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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67 </when>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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68 <when value="fasta">
3
27f5da0a6bd9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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69 <param name="input_fasta" multiple="True" type="data" format="fasta" label="Input file in FASTA format"/>
0
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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70 </when>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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71 <when value="fastq">
3
27f5da0a6bd9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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72 <param name="input_fastq" multiple="True" type="data" format="fastq" label="Input file in FASTQ format"/>
0
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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73 <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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74 falsevalue=""
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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75 label="Ignore read quality?"
3
27f5da0a6bd9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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76 help="Do not use read quality as part of checksum. (--no-quality)"/>
0
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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77 <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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78 falsevalue=""
3
27f5da0a6bd9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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79 label="List of fastq files are not paired-end reads?"
27f5da0a6bd9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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80 help="(--no-paired)" />
0
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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81 </when>
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82 </conditional>
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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83 <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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84 falsevalue=""
c76494b4ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 2749adf8099bbdea4f61759201b3f2b92db5ff0f
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85 label="Ignore readnames?"
3
27f5da0a6bd9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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86 help="Do not use read names as part of checksum. (--no-readnames)"/>
0
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87
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88 </inputs>
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89 <outputs>
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90 <data name="output" format="txt" from_work_dir="./output.txt"
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91 label="${tool.name} on ${on_string}">
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92 </data>
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93 </outputs>
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94 <tests>
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95 <test>
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96 <param name="input_bam" value="Example.bam" ftype="bam"/>
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97 <param name="tool_choice" value="bam"/>
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98 <output name="output" file="output1_bam.txt" ftype="txt"/>
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99 </test>
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100 <test>
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101 <param name="input_fasta" value="UnAligSeq24606.fasta" ftype="fasta"/>
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102 <param name="tool_choice" value="fasta"/>
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103 <param name="readnames" value="--no-readnames"/>
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104 <output name="output" file="output2_fasta.txt" ftype="txt"/>
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105 </test>
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106 <test>
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107 <param name="input_fastq" value="1_mismatch.fastq,2_mismatch.fastq" ftype="fastq"/>
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108 <param name="tool_choice" value="fastq"/>
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109 <param name="noQuality" value="--no-quality"/>
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110 <output name="output" file="output3_fastq.txt" ftype="txt"/>
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111 </test>
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112 <test>
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113 <param name="input_fastq" value="1_mismatch.fastq,2_mismatch.fastq" ftype="fastq"/>
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114 <param name="tool_choice" value="fastq"/>
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115 <output name="output" file="output4_fastq.txt" ftype="txt"/>
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116 </test>
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117 </tests>
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118 <help><![CDATA[
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119
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120 **WHAT IT DOES**
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121
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122 Hash BAM and FASTQ files to verify data integrity
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123
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124 For each pair of reads in a BAM or FASTQ file we compute a hash value composed of the readname,
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125 whether it is first or last in pair, sequence and quality value. All the hash values are summed
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126 up so the result is independent of the ordering within the files. The result can be compared to
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127 verify that the pair of FASTQ files contain the same read information as the aligned BAM file.
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128
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129 -----
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130
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131 **BAM**
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132
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133 processes a number of BAM files. BAM files are assumed to contain paired end reads.
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134 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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135
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136 -----
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137
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138 **FASTA**
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139
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140 processes a number of FASTA files. All FASTA files are assumed to be single end reads with no quality information.
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141 To compare to a BAM file, run bamhash_checksum_bam --no-paired --no-quality
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142
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143 -----
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144
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145
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146 **FASTQ**
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147
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148 processes a number of FASTQ files. FASTQ files are assumed to contain paired end reads,
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149 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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150
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151
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152 -----
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153
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154
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155 **BamHash** is a Free and Open Source Software, see more details on the BamHash github_ Website.
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156
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157 .. _github: https://github.com/DecodeGenetics/BamHash
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158
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159 ]]></help>
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160 <citations></citations>
0
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161 </tool>