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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:25:24 +0000
parents c89806670ab9
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
2
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4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
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5 <yield/>
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6 </requirements>
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7 </xml>
7
c89806670ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit cd62639660bef041ba14ecff337fb98e84e75d8a
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8 <!-- NOTE: for some tools only the version of the requirement but not the
c89806670ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit cd62639660bef041ba14ecff337fb98e84e75d8a
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9 tool's version is controlled by the TOOL_VERSION token
c89806670ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit cd62639660bef041ba14ecff337fb98e84e75d8a
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10 (because their version is ahead of the requirement version ..
c89806670ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit cd62639660bef041ba14ecff337fb98e84e75d8a
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11 please only bump the minor version in order to let the requirement
c89806670ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit cd62639660bef041ba14ecff337fb98e84e75d8a
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12 version catch up eventually). To find the tools check:
c89806670ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit cd62639660bef041ba14ecff337fb98e84e75d8a
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13 `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
8
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14 <token name="@TOOL_VERSION@">1.20</token>
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c89806670ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit cd62639660bef041ba14ecff337fb98e84e75d8a
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15 <token name="@VERSION_SUFFIX@">2</token>
8
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16 <token name="@PROFILE@">22.05</token>
5
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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17 <token name="@FLAGS@"><![CDATA[
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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18 #set $flags = 0
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19 #if $filter
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20 #set $flags = sum(map(int, str($filter).split(',')))
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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21 #end if
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22 ]]></token>
2
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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23 <token name="@PREPARE_IDX@"><![CDATA[
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c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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24 ##prepare input and indices
2
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25 ln -s '$input' infile &&
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26 #if $input.is_of_type('bam'):
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27 #if str( $input.metadata.bam_index ) != "None":
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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28 ln -s '${input.metadata.bam_index}' infile.bai &&
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29 #else:
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30 samtools index infile infile.bai &&
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31 #end if
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32 #elif $input.is_of_type('cram'):
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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33 #if str( $input.metadata.cram_index ) != "None":
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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34 ln -s '${input.metadata.cram_index}' infile.crai &&
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35 #else:
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36 samtools index infile infile.crai &&
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37 #end if
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38 #end if
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39 ]]></token>
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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40 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
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41 ##prepare input and indices
2
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42 #for $i, $bam in enumerate( $input_bams ):
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43 ln -s '$bam' '${i}' &&
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44 #if $bam.is_of_type('bam'):
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45 #if str( $bam.metadata.bam_index ) != "None":
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46 ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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47 #else:
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48 samtools index '${i}' '${i}.bai' &&
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49 #end if
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50 #elif $bam.is_of_type('cram'):
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51 #if str( $bam.metadata.cram_index ) != "None":
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52 ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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53 #else:
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54 samtools index '${i}' '${i}.crai' &&
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55 #end if
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56 #end if
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57 #end for
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58 ]]></token>
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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59 <token name="@PREPARE_FASTA_IDX@"><![CDATA[
6
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60 ## Make the user-selected reference genome, if any, accessible through
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61 ## a shell variable $reffa, index the reference if necessary, and make
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62 ## the fai-index file available through a shell variable $reffai.
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63
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64 ## For a cached genome simply sets the shell variables to point to the
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65 ## genome file and its precalculated index.
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66 ## For a genome from the user's history, if that genome is a plain
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67 ## fasta file, the code creates a symlink in the pwd, creates the fai
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68 ## index file next to it, then sets the shell variables to point to the
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69 ## symlink and its index.
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70 ## For a fasta.gz dataset from the user's history, it tries the same,
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71 ## but this will only succeed if the file got compressed with bgzip.
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72 ## For a regular gzipped file samtools faidx will fail, in which case
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73 ## the code falls back to decompressing to plain fasta before
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74 ## reattempting the indexing.
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75 ## Indexing of a bgzipped file produces a regular fai index file *and*
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76 ## a compressed gzi file. The former is identical to the fai index of
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77 ## the uncompressed fasta.
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78
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79 ## If the user has not selected a reference (it's an optional parameter
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80 ## in some samtools wrappers), a cheetah boolean use_ref is set to
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81 ## False to encode that fact.
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82
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83 #set use_ref=True
2
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84 #if $addref_cond.addref_select == "history":
6
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85 #if $addref_cond.ref.is_of_type('fasta'):
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86 reffa="reference.fa" &&
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87 ln -s '${addref_cond.ref}' \$reffa &&
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88 samtools faidx \$reffa &&
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89 #else:
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90 reffa="reference.fa.gz" &&
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91 ln -s '${addref_cond.ref}' \$reffa &&
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92 {
92ec40abcdcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit c5ded4208dd70e88596ddc725795a2401773f02d"
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93 samtools faidx \$reffa ||
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94 {
92ec40abcdcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit c5ded4208dd70e88596ddc725795a2401773f02d"
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95 echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 &&
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96 gzip -dc \$reffa > reference.fa &&
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97 reffa="reference.fa" &&
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98 samtools faidx \$reffa;
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99 }
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100 } &&
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101 #end if
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102 reffai=\$reffa.fai &&
2
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103 #elif $addref_cond.addref_select == "cached":
6
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104 ## in case of cached the absolute path is used which allows to read
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105 ## a cram file without specifying the reference
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106 reffa='${addref_cond.ref.fields.path}' &&
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107 reffai=\$reffa.fai &&
2
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108 #else
6
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109 #set use_ref=False
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110 #end if
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111 ]]></token>
5
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112
7
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113 <xml name="optional_reference" token_help="" token_argument="">
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114 <conditional name="addref_cond">
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115 <param name="addref_select" type="select" label="Use a reference sequence">
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116 <help>@HELP@</help>
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117 <option value="no">No</option>
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118 <option value="history">Use a genome/index from the history</option>
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119 <option value="cached">Use a built-in genome</option>
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120 </param>
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121 <when value="no"/>
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122 <when value="history">
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123 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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124 </when>
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125 <when value="cached">
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126 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
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127 <options from_data_table="fasta_indexes">
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128 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
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129 </options>
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130 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/>
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131 </param>
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132 </when>
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133 </conditional>
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134 </xml>
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135 <xml name="mandatory_reference" token_help="" token_argument="">
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136 <conditional name="addref_cond">
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137 <param name="addref_select" type="select" label="Use a reference sequence">
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138 <help>@HELP@</help>
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139 <option value="history">Use a genome/index from the history</option>
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140 <option value="cached">Use a built-in genome</option>
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141 </param>
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142 <when value="history">
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143 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
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144 </when>
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145 <when value="cached">
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146 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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147 <options from_data_table="fasta_indexes">
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148 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
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149 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
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150 </options>
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151 </param>
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152 </when>
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153 </conditional>
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154 </xml>
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155
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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156
2
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157 <token name="@ADDTHREADS@"><![CDATA[
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158 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
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159 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
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160 ]]></token>
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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161 <token name="@ADDMEMORY@"><![CDATA[
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162 ##compute the number of memory available to samtools sort (-m)
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163 ##use only 75% of available: https://github.com/samtools/samtools/issues/831
5
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164 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
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165 ((addmemory=addmemory*75/100)) &&
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166 ]]></token>
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167 <xml name="seed_input">
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168 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
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169 </xml>
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170 <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false">
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171 <option value="1" selected="@S1@">Read is paired</option>
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172 <option value="2" selected="@S2@">Read is mapped in a proper pair</option>
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173 <option value="4" selected="@S4@">Read is unmapped</option>
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174 <option value="8" selected="@S8@">Mate is unmapped</option>
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175 <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option>
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176 <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option>
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177 <option value="64" selected="@S64@">Read is the first in a pair</option>
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178 <option value="128" selected="@S128@">Read is the second in a pair</option>
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179 <option value="256" selected="@S256@">Alignment of the read is not primary</option>
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180 <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option>
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181 <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option>
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182 <option value="2048" selected="@S2048@">Alignment is supplementary</option>
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183 </xml>
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184
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185 <!-- region specification macros and tokens for tools that allow the specification
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186 of region by bed file / space separated list of regions -->
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187 <token name="@REGIONS_FILE@"><![CDATA[
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188 #if $cond_region.select_region == 'tab':
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189 -t '$cond_region.targetregions'
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190 #end if
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191 ]]></token>
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192 <token name="@REGIONS_MANUAL@"><![CDATA[
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193 #if $cond_region.select_region == 'text':
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194 #for $i, $x in enumerate($cond_region.regions_repeat):
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195 '${x.region}'
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196 #end for
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197 #end if
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198 ]]></token>
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199 <xml name="regions_macro">
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200 <conditional name="cond_region">
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201 <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
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202 <option value="no" selected="True">No</option>
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203 <option value="text">Manualy specify regions</option>
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204 <option value="tab">Regions from tabular file</option>
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205 </param>
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206 <when value="no"/>
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207 <when value="text">
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208 <repeat name="regions_repeat" min="1" default="1" title="Regions">
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209 <param name="region" type="text" label="region" help="format chr:from-to">
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210 <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator>
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211 </param>
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212 </repeat>
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213 </when>
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214 <when value="tab">
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215 <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" />
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216 </when>
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217 </conditional>
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218 </xml>
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219
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220 <xml name="citations">
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221 <citations>
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222 <citation type="doi">10.1093/gigascience/giab008</citation>
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223 </citations>
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224 </xml>
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225 <xml name="version_command">
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226 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
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227 </xml>
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228 <xml name="stdio">
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229 <stdio>
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230 <exit_code range="1:" level="fatal" description="Error" />
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231 </stdio>
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232 </xml>
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233 </macros>