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annotate bamhash.xml @ 0:63f6f42d112b draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
author bgruening
date Thu, 17 Sep 2015 08:00:35 -0400
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63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
bgruening
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1 <tool id="bamhash" name="BamHash" version="1.1">
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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2 <description>Hash BAM and FASTQ files to verify data integrity</description>
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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3 <requirements>
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4 <requirement type="package" version="1.1">bamhash</requirement>
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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5 </requirements>
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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6 <stdio>
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7 <exit_code range="1:" />
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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8 <exit_code range=":-1" />
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9 <regex match="Error:" />
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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10 <regex match="Exception:" />
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11 </stdio>
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12 <version_command>bamhash_checksum_fastq --version</version_command>
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13 <command><![CDATA[
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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14 #if $tool.tool_choice=="bam":
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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15 #for $counter, $file in enumerate($tool.input_bam):
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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16 ln -s "${file}" "${counter}.bam" ## 1.bam ... 2.bam
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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17 &&
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18 #end for
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19 bamhash_checksum_bam
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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20 $tool.noQuality_bam
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21 $tool.noPaired_bam
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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22 #for $counter, $filename in enumerate($tool.input_bam):
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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23 "${counter}.bam"
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24 #end for
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25 #elif $tool.tool_choice=="fastq":
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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26 #for $counter, $file in enumerate($tool.input_fastq):
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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27 ln -s "${file}" "${counter}.fastq" ## 1.fastq ... 2.fastq
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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28 &&
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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29 #end for
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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30 bamhash_checksum_fastq
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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31 $tool.noQuality_fastq
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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32 $tool.noPaired_fastq
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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33 #for $counter, $filename in enumerate($tool.input_fastq):
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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34 "${counter}.fastq"
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35 #end for
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36 #elif $tool.tool_choice=="fasta":
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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37 #for $counter, $file in enumerate($tool.input_fasta):
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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38 ln -s "${file}" "${counter}.fasta" ## 1.fasta ... 2.fasta
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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39 &&
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40 #end for
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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41 bamhash_checksum_fasta
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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42 #for $counter, $filename in enumerate($tool.input_fasta):
63f6f42d112b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bamhash commit 7aa0b566d492b1830c0bd2e54ddf4a26be95f76d
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43 "${counter}.fasta"
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44 #end for
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45 #end if
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46 $readnames
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47 > output.txt
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48 ]]></command>
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49 <inputs>
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50 <conditional name="tool">
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51 <param name="tool_choice" type="select" label="Choose file type:"
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52 help="">
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53 <option value="bam">BAM file(s)</option>
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54 <option value="fastq">FASTQ file(s)</option>
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55 <option value="fasta">FASTA file(s)</option>
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56 </param>
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57 <when value="bam">
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58 <param name="input_bam" multiple="True" type="data" format="bam" label="Input file in BAM format"/>
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59 <param name="noQuality_bam" type="boolean" checked="false" truevalue="--no-quality"
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60 falsevalue=""
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61 label="Ignore read quality?"
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62 help="Do not use read quality as part of checksum. (--no-quality)"/>
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63 <param name="noPaired_bam" type="boolean" checked="false" truevalue="--no-paired"
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64 falsevalue=""
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65 label="Bam files were not generated with paired-end reads?"
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66 help="(--no-paired)" />
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67 </when>
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68 <when value="fasta">
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69 <param name="input_fasta" multiple="True" type="data" format="fasta" label="Input file in FASTA format"/>
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70 </when>
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71 <when value="fastq">
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72 <param name="input_fastq" multiple="True" type="data" format="fastq" label="Input file in FASTQ format"/>
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73 <param name="noQuality_fastq" type="boolean" checked="false" truevalue="--no-quality"
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74 falsevalue=""
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75 label="Ignore read quality?"
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76 help="Do not use read quality as part of checksum. (--no-quality)"/>
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77 <param name="noPaired_fastq" type="boolean" checked="false" truevalue="--no-paired"
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78 falsevalue=""
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79 label="List of fastq files are not paired-end reads?"
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80 help="(--no-paired)" />
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81 </when>
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82 </conditional>
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83 <param name="readnames" type="boolean" checked="false" truevalue="--no-readnames"
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84 falsevalue=""
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85 label="Ignore readnames?"
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86 help="Do not use read names as part of checksum. (--no-readnames)"/>
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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>
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161 </citations>
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162 </tool>