Mercurial > repos > nml > smalt

annotate smalt_map.xml @ 2:5ba47ab90254 draft default tip

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"planemo upload for repository https://sourceforge.net/projects/smalt/ commit e795229a49483da24e80fab0809216557de09840"
author nml
date Thu, 25 Jun 2020 16:45:36 -0400
parents fae9ec82e10f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
5ba47ab90254 "planemo upload for repository https://sourceforge.net/projects/smalt/ commit e795229a49483da24e80fab0809216557de09840"
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1 <tool id="smalt" name="smalt" version="@VERSION@+galaxy1">
0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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2 <description>Map query reads (FASTA/FASTQ) format onto the reference sequences</description>
1
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
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3 <macros>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
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4 <token name="@VERSION@">0.7.6</token>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
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5 <token name="@INPUT_TYPES@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
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6 </macros>
0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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7 <requirements>
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fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
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8 <requirement type="package" version="@VERSION@">smalt</requirement>
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5ba47ab90254 "planemo upload for repository https://sourceforge.net/projects/smalt/ commit e795229a49483da24e80fab0809216557de09840"
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9 <requirement type="package" version="1.10">samtools</requirement>
0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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10 </requirements>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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11 <stdio>
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12 <exit_code range="1:" level="fatal" description="Unknown error" />
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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13 <regex match="Command line error"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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14 source="stdout"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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15 level="fatal"
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16 description="You cannot do that!! What were you thinking!" />
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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17 <regex match="ERROR"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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18 source="stderr"
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19 level="fatal"
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20 description="You cannot do that!! What were you thinking!" />
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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21 </stdio>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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22 <command>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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23 <![CDATA[
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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24 ## prepare smalt index
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25 smalt index
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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26
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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27 #if $k:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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28 -k "$k"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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29 #end if
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30
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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31 #if $s:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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32 -s "$s"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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33 #end if
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34
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35 'temp' "$reference" &&
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36
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37 smalt map
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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38
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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39 -o $output
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40
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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41 #if $oformat.outformat == "sam":
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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42 #if $oformat.samOptions:
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43 -f "$oformat.outformat:$oformat.samOptions"
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44 #else
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45 -f "$oformat.outformat"
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46 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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47 #elif $oformat.outformat == "bam":
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48 #if $oformat.bamOptions:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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49 -f "$oformat.outformat:$oformat.bamOptions"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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50 #else
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51 -f "$oformat.outformat"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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52 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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53 #else
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54 -f "$oformat.outformat"
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55 #end if
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56
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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57
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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58
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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59 -n \${GALAXY_SLOTS:-2}
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60
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
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61 #if $singlePaired.sPaired != "single":
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62 -l $singlePaired.pairtype
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63 #end if
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64
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65
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66 #if $mincover:
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67 -c "$mincover"
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68 #end if
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69
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70 #if $scordiff:
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71 -d "$scordiff"
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72 #end if
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73
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74 #if $insfil:
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75 -g "$insfil"
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76 #end if
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77
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78 #if $insertmax:
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79 -i "$insertmax"
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80 #end if
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81
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82 #if $insertmin:
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83 -j "$insertmin"
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84 #end if
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85
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86 #if $minscor:
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87 -m "$minscor"
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88 #end if
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89
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90 #if $minbasq:
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91 -q "$minbasq"
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92 #end if
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93
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94 #if $seed:
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95 -r "$seed"
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96 #end if
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97
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98 #if $sw_weighted:
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99 -w
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100 #end if
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101
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102 #if $search_harder:
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103 -x
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104 #end if
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105
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106 #if $minid:
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107 -y "$minid"
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108 #end if
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109
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110
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111 'temp'
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112
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113 #if $singlePaired.sPaired == "single":
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114 $singlePaired.sInput1
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115 #elif $singlePaired.sPaired == "paired":
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116 $singlePaired.pInput1 $singlePaired.pInput2
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117 #elif $singlePaired.sPaired == "collections":
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118 $singlePaired.fastq_collection.forward $singlePaired.fastq_collection.reverse
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119 #end if
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120
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121
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122 #if $oformat.outformat == "bam":
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123 && samtools sort -@ \${GALAXY_SLOTS:-1} $output -o sorted && mv sorted $output
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124 #end if
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125
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126
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127 ]]>
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128 </command>
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129
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130
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131 <inputs>
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132 <conditional name="singlePaired">
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133 <param name="sPaired" type="select" label="What is the library type?">
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134 <option value="single">Single-end</option>
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135 <option value="paired">Paired-end</option>
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136 <option value="collections">Paired-end Collections</option>
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137 </param>
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138 <when value="single">
1
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139 <param name="sInput1" type="data" format="@INPUT_TYPES@" label="Single end illumina fastq file" optional="false"/>
0
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140 </when>
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141 <when value="paired">
1
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142 <param name="pInput1" type="data" format="@INPUT_TYPES@" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
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143 <param name="pInput2" type="data" format="@INPUT_TYPES@" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/>
0
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144 <param name="pairtype" type="select" label="Pair Type" help="Type of read pair library">
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145 <option value="pe">Illumina paired-end (short inserts)</option>
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146 <option value="mp">Illumina mate-pair library (long inserts)</option>
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147 <option value="pp">Mate-pair sequenced on the same strand</option>
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148 </param>
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149 </when>
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150 <when value="collections">
1
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151 <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="@INPUT_TYPES@" collection_type="paired" />
0
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152 <param name="pairtype" type="select" label="Pair Type" help="Type of read pair library">
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153 <option value="pe">Illumina paired-end (short inserts)</option>
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154 <option value="mp">Illumina mate-pair library (long inserts)</option>
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155 <option value="pp">Mate-pair sequenced on the same strand</option>
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156 </param>
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157 </when>
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158
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159 </conditional>
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160
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161
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162
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163 <!-- reference genome -->
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164 <param name="reference" type="data" format="fasta" label="Select fasta reference"/>
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165 <param name="k" type="integer" value="13" label="K-mer size" help="Specifies the word length. [wordlen] is an integer within the limits. between 3 and 20. The default word length is 13" max="20" min="3"/>
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166 <param name="s" type="integer" optional="true" label="Step size" help="Specifies how many bases are skipped between indexed words."/>
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167
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168
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169 <param name="mincover" type="text" label="Mincover" help="Only consider mappings where the k-mer word seeds cover the query read to a minimum extent"/>
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170 <param name="scordiff" type="text" label="Scordiff" help="Set a threshold of the Smith-Waterman alignment score relative to the maximum score"/>
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171 <conditional name="oformat">
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172 <param name="outformat" type="select" label="Format" help="">
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173 <option value="cigar">cigar</option>
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174 <option value="sam" selected="true">sam</option>
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175 <option value="ssaha">ssaha</option>
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176 <option value="bam">bam</option>
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177 </param>
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178 <when value="sam">
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179 <param name="samOptions" type="select" display="checkboxes" label="Sam Options" multiple="true">
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180 <option value="nohead">No Header</option>
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181 <option value="clip">Hard Clip</option>
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182 </param>
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183 </when>
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184 <when value="bam">
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185 <param name="bamOptions" type="select" display="checkboxes" label="Bam Options" multiple="true">
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186 <option value="clip">Hard Clip</option>
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187 </param>
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188 </when>
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189 <when value="cigar">
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190 </when>
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191 <when value="ssaha">
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192 </when>
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193 </conditional>
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194 <param name="insfil" type="data" optional="true" label="Distribution insert sizes " help="Use the distribution of insert sizes stored in the file [insfil. Thisfile is in ASCII format and can be generated using the 'sample'" format="sam"/>
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195 <param name="insertmax" type="text" label="Maximum insert size (only in paired-end mode). " help="Maximum insert size (only in paired-end mode). The default is 500."/>
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196 <param name="insertmin" type="text" label="Minimum insert size (only in paired-end mode). " help="Minimum insert size (only in paired-end mode). The default is 0."/>
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197
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198
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199 <param name="minscor" type="text" label="Sets an absolute threshold of the Smith-Waterman scores." help="Mappings with scores below that threshold will not be reported. The default is &#060; minscor &#062; = &#060; wordlen &#062; + &#060; stepsiz &#062; - 1"/>
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200
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201 <param name="minbasq" type="text" label="Sets a base quality threshold (0 &#060;= minbasq &#060;= 10, default 0)" help="K-mer words of the read with nucleotides that have a base quality below this threshold are not looked up in the hash index."/>
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202
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203 <param name="seed" type="text" label="If the there are multiple mappings with the same best alignment score report one picked at random." help="is an integer >= 0 used to seed the pseudo-random genarator."/>
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204
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205 <param name="sw_weighted" type="boolean" label="Smith-Waterman scores are complexity weighted."/>
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206
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207 <param name="search_harder" type="boolean" label="This flag triggers a more exhaustive search for alignments at the cost of decreased speed" help="In paired-end mode each mate is mapped independently. (By default the mate with fewer hits in the hash index is mapped first and the vicinity is searched for mappings of its mate.)"/>
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208
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209 <param name="minid" type="text" label="Sets an identity threshold for a mapping to be reported (default: 0)." help="specifies the number of exactly matching nucleotides either as a positive integer or as a fraction of the read length (&#062;= 1.0)."/>
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210 </inputs>
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211
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212 <outputs>
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213 <data name="output" format="cigar" >
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214 <change_format>
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215 <when input="oformat.outformat" value="cigar" format="cigar"/>
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216 <when input="oformat.outformat" value="sam" format="sam"/>
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217 <when input="oformat.outformat" value="ssaha" format="ssaha"/>
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218 <when input="oformat.outformat" value="bam" format="bam"/>
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219 </change_format>
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220 </data>
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221 </outputs>
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222 <tests>
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223 <test>
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224 <param name="sPaired" value="paired"/>
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225 <param name="pInput1" value="ecoli_1K_1.fq"/>
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226 <param name="pInput2" value="ecoli_1K_2.fq"/>
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227 <param name="pairtype" value="pe"/>
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228 <param name="source" value="history"/>
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229 <param name="reference" value="contigs.fasta"/>
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230 <param name="outformat" value="sam"/>
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231 <output name="output">
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232 <assert_contents>
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233 <has_text text="SN:NODE_1_length_1000_cov_140.620106" />
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234 </assert_contents>
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235 </output>
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236 </test>
1
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237 <test>
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238 <param name="sPaired" value="paired"/>
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239 <param name="pInput1" value="ecoli_1K_1.fq.gz"/>
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240 <param name="pInput2" value="ecoli_1K_2.fq.gz"/>
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241 <param name="pairtype" value="pe"/>
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242 <param name="source" value="history"/>
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243 <param name="reference" value="contigs.fasta"/>
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244 <param name="outformat" value="sam"/>
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245 <output name="output">
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246 <assert_contents>
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247 <has_text text="SN:NODE_1_length_1000_cov_140.620106" />
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248 </assert_contents>
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249 </output>
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250 </test>
0
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251 </tests>
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252 <help>
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253
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254 **What it does**
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255
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256 SMALT is a pairwise sequence alignment program for the experimentingcient mapping of DNA sequencing reads onto genomic reference sequences. It uses a combination of short-word hashing and dynamic programming. Most types of sequencing platforms are supported including paired-end sequencing reads.
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257
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258
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259 ------
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260
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261
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262 **Know what you are doing**
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263
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264 .. class:: warningmark
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265
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266 There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
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267
1
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268 .. __: https://www.sanger.ac.uk/tool/smalt-0/
0
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269
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270 ------
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271
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272 **Input formats**
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273
1
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274 SMALT accepts files in Sanger FASTQ format (galaxy type *fastqsanger* or *fastqsanger.gz*). Use the FASTQ Groomer to prepare your files.
0
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275
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276 ------
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277
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278
1
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279 Please cite the website "https://www.sanger.ac.uk/tool/smalt-0/".
0
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280
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281 ------
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282
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283
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284 -a Output explicit alignments along with the mapping coordinates.
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285
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286 -c &#060;mincover INT&#062;
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287 Only consider mappings where the k-mer word seeds cover the query read to
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288 a minimum extent. If &#060;mincover&#062; is an integer or floating point &#062; 1.0, at
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289 least this many bases of the read must be covered by k-mer word seeds. If
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290 &#060;mincover&#062; is a floating point &#060;= 1.0, it specifies the fraction of the
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291 query read length that must be covered by k-mer word seeds. This option
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292 is only valid in conjunction with the '-x' flag.
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293
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294 -d &#060;scordiff INT&#062;
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295 Set a threshold of the Smith-Waterman alignment score relative to the
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296 maximum score. When mapping single reads, all alignments are reported
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297 that have Smith-Waterman scores within &#060;scorediff&#062; of the maximum.
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298 Mappings with lower scores are skipped. If &#060;scorediff&#062; is set to to a
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299 value &#060; 0, all alignments are printed that have scores above the
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300 threshold specified with the '-m &#060;minscor&#062;' option.
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301 For paired reads, only a value of 0 is supported. With the option '-d 0'
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302 all aligments (pairings) with the best score are output. By default
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303 (without the option '-d 0') single reads/mates with multiple best mappings
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304 are reported as 'not mapped'.
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305
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306 -f &#060;ouform STR&#062;
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307 Specifies the output format. &#060;ouform&#062; can be either 'sam'(default),
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308 'cigar', 'gff' or 'ssaha'. Optional extension 'sam:nohead,x,clip'
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309 (see manual). Support for BAM format is dependent on additional
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310 libraries (not installed).
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311
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312 -F &#060;inform STR&#062;
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313 Specifies the input format. The only available format is fastq (default).
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314 Support for BAM and SAM formats (see: samtools.sourceforge.net) depends
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315 on additional libraries (not installed).
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316
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317 -g &#060;insfil STR&#062;
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318 Use the distribution of insert sizes stored in the file &#060;insfil&#062;. This
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319 file is in ASCII format and can be generated using the 'sample' task see
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320 'smalt sample -H' for help).
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321
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322 -H Print these instructions.
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323
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324 -i &#060;insert_max INT&#062;
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325 Maximum insert size (only in paired-end mode). The default is 500.
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326
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327 -j &#060;insert_min INT&#062;
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328 Minimum insert size (only in paired-end mode). The default is 0.
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329
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330 -l &#060;pairtyp STR&#062;
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331 Type of read pair library. &#060;pairtyp&#062; can be either 'pe', i.e. for
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332 the Illumina paired-end library for short inserts ( \|&#8212;&#062; &#060;&#8212;\| ). 'mp'
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333 for the Illumina mate-pair library for long inserts ( &#060;&#8212;\| \|&#8212;&#062; ) or
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334 'pp' for mates sequenced on the same strand ( \|&#8212;&#062; \|&#8212;&#062; ). 'pe' is the
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335 default.
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336
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337 -m &#060;minscor INT&#062;
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338 Sets an absolute threshold of the Smith-Waterman scores. Mappings with
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339 scores below that threshold will not be reported. The default is
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340 &#060;minscor&#062; = &#060;wordlen&#062; + &#060;stepsiz&#062; - 1.
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341
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342 -n &#060;nthreads INT&#062;
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343 Run smalt using mutiple threads. &#060;nthread&#062; is the number of additional
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344 threads forked. The order of the reads in the input files is not preserved
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345 for the output unless '-O' is also specified.
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346
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347 -o &#060;oufilnam STR&#062;
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348 Write mapping output (e.g. SAM lines) to a separate file. If this option
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349 is not specified, mappings are written to standard output.
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350
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351 -O Output mappings in the order of the reads in the input files when using
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352 multiple threads (option '-n &#060;nthreads&#062;').
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353
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354
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355 -p Report partial alignments if they are complementary on the read (split
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356 reads).
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357
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358 -q &#060;minbasq INT&#062;
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359 Sets a base quality threshold (0 &#060;= minbasq &#060;= 10, default 0).
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360 K-mer words of the read with nucleotides that have a base quality below
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361 this threshold are not looked up in the hash index.
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362
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363 -r &#060;seed INT&#062;
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364 If &#060;seed&#062; &#062;= 0 report an alignment selected at random where there are
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365 multiple mappings with the same best alignment score. With &#060;seed&#062; = 0
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366 (default) a seed is derived from the current calendar time. If &#060;seed&#062;
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367 &#060; 0 reads with multiple best mappings are reported as 'not mapped'.
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368
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369 -S &#060;scorspec STR&#062;
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370 Specify alignment penalty scores for a match or mismatch (substitution),
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371 or for opening or extending a gap. &#060;scorspec&#062; is a comma speparated
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372 list of integer assigments to one or more of the following variables:
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373 match, subst, gapopen, gapext, i.e. 'gapopen=-5,gapext=-4' (no spaces
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374 allowed in &#060;scorespec&#062;). Default:'match=1,subst=-2,gapopen=-4,gapext=-3'
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375
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376 -w Smith-Waterman scores are complexity weighted.
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377
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378 -x This flag triggers a more exhaustive search for alignments at the cost
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379 of speed. In paired-end mode each mate is mapped independently.(By
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380 default the mate with fewer hits in the hash index is mapped first and
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381 the vicinity is searched for mappings of its mate.)
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382
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383 -y &#060;minid FLT&#062;
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384 Sets an identity threshold for a mapping to be reported (default: 0).
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385 &#060;minid&#062; specifies the number of exactly matching nucleotides either as
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386 a positive integer or as a fraction of the read length (&#060;= 1.0).
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387 </help>
1
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388 <citations>
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389 <citation type="bibtex">
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390 @misc{smaltcitation,
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391 author = {Ponstigl, Hannes},
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392 year = {2010},
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393 title = {smalt},
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394 publisher = {Wellcome Trust Sanger Institute, Cambridge, UK},
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395 journal = {Online},
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396 url = {https://www.sanger.ac.uk/tool/smalt-0/}
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397 }</citation>
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398 </citations>
0
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399 </tool>