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annotate samtools_sort.xml @ 2:f56bdb93ae58 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
author iuc
date Wed, 19 Sep 2018 09:53:49 -0400
parents cab3f8d35989
children e613c1ad4c4c
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f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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1 <tool id="samtools_sort" name="Samtools sort" version="2.0.2">
1
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2 <description>order of storing aligned sequences</description>
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3 <macros>
1
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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4 <import>macros.xml</import>
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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5 </macros>
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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6 <expand macro="requirements"/>
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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9 <command><![CDATA[
2
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10 @ADDTHREADS@
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11 @ADDMEMORY@
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cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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12 samtools sort
2
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13 -@ \$addthreads
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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14 -m \$addmemory"M"
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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15 ###if str(compression):
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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16 ## -l '$compression'
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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17 ###end if
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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18 $prim_key_cond.prim_key_select
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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19 #if $prim_key_cond.prim_key_select == '-t':
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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20 $prim_key_cond.tag
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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21 $prim_key_cond.sec_key_select
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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22 #end if
1
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23 -O bam
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24 -T sorttmp
1
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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25 '${input1}'
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26 > '${output1}'
1
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27 ]]></command>
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28 <inputs>
2
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29 <param name="input1" type="data" format="sam,bam,cram" label="BAM File" />
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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30 <conditional name="prim_key_cond">
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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31 <param name="prim_key_select" type="select" label="Primary sort key">
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32 <option value="">coordinate</option>
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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33 <option value="-n">name (-n)</option>
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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34 <option value="-t">tag (-t)</option>
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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35 </param>
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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36 <when value=""/>
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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37 <when value="-n"/>
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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38 <when value="-t">
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39 <param name="tag" type="text" optional="false" argument="-t" label="Alignment tag"/>
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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40 <param name="sec_key_select" type="select" label="Secondary sort key">
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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41 <option value="">coordinate</option>
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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42 <option value="-n">name (-n)</option>
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43 </param>
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44 </when>
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45 </conditional>
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46 <!--<param name="compression" type="integer" argument="-l" optional="True" min="0" max="9" label="compression level" help="0 (uncompressed) to 9 (best)"/>-->
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47 </inputs>
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48 <outputs>
2
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49 <data name="output1" format="bam">
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50 <change_format>
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51 <when input="prim_key_cond.prim_key_select" value="" format="bam" />
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52 <when input="prim_key_cond.prim_key_select" value="-n" format="qname_sorted.bam" />
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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53 <when input="prim_key_cond.prim_key_select" value="-t" format="unsorted.bam" />
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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54 </change_format>
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55 </data>
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56 </outputs>
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57 <tests>
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58 <!-- tests from https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2464 -->
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59 <!-- # Pos sort -->
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60 <test>
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61 <param name="input1" value="test_input_1_a.bam" ftype="bam" />
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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62 <output name="output1" file="pos.sort.expected.bam" ftype="bam"/>
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63 </test>
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64 <!-- test_cmd($opts, out=>"sort/pos.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} $$opts{path}/dat/test_input_1_a.bam -O SAM -o -"); -->
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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65
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66 <!-- # Name sort -->
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67 <test>
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68 <param name="input1" value="test_input_1_a.bam" ftype="bam" />
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69 <conditional name="prim_key_cond">
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70 <param name="prim_key_select" value="-n"/>
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71 </conditional>
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72 <output name="output1" file="name.sort.expected.bam" ftype="qname_sorted.bam"/>
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73 </test>
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74 <!-- test_cmd($opts, out=>"sort/name.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -n $$opts{path}/dat/test_input_1_a.bam -O SAM -o -");-->
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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75
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76 <!-- # Tag sort (RG) (considers output and name sorted) -->
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77 <test>
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78 <param name="input1" value="test_input_1_a.bam" ftype="bam" />
f56bdb93ae58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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79 <conditional name="prim_key_cond">
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80 <param name="prim_key_select" value="-t"/>
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81 <param name="tag" value="RG"/>
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82 </conditional>
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83 <output name="output1" file="tag.rg.sort.expected.bam" ftype="unsorted.bam"/>
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84 </test>
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85 <!--test_cmd($opts, out=>"sort/tag.rg.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -t RG $$opts{path}/dat/test_input_1_a.bam -O SAM -o -");-->
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86
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87 <!-- # Tag sort (RG); secondary by name -->
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88 <test>
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89 <param name="input1" value="test_input_1_a.bam" ftype="bam" />
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90 <conditional name="prim_key_cond">
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91 <param name="prim_key_select" value="-t"/>
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92 <param name="tag" value="RG"/>
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93 <param name="sec_key_select" value="-n"/>
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94 </conditional>
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95 <output name="output1" file="tag.rg.n.sort.expected.bam" ftype="unsorted.bam"/>
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96 </test>
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97 <!--test_cmd($opts, out=>"sort/tag.rg.n.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -n -t RG $$opts{path}/dat/test_input_1_a.bam -O SAM -o -");-->
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98
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99 <!-- # Tag sort (AS) -->
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100 <test>
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101 <param name="input1" value="test_input_1_a.bam" ftype="bam" />
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102 <conditional name="prim_key_cond">
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103 <param name="prim_key_select" value="-t"/>
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104 <param name="tag" value="AS"/>
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105 <param name="sec_key_select" value=""/>
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106 </conditional>
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107 <output name="output1" file="tag.as.sort.expected.bam" ftype="unsorted.bam"/>
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108 </test>
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109 <!--test_cmd($opts, out=>"sort/tag.as.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -t AS $$opts{path}/dat/test_input_1_d.sam -O SAM -o -");-->
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110
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111 <!-- # Tag sort (FI) -->
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112 <test>
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113 <param name="input1" value="test_input_1_a.bam" ftype="bam" />
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114 <conditional name="prim_key_cond">
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115 <param name="prim_key_select" value="-t"/>
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116 <param name="tag" value="FI"/>
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117 </conditional>
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118 <output name="output1" file="tag.fi.sort.expected.bam" ftype="unsorted.bam"/>
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119 </test>
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120 <!--test_cmd($opts, out=>"sort/tag.fi.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -t FI $$opts{path}/dat/test_input_1_d.sam -O SAM -o -");-->
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121
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122 <!-- tests from old version -->
0
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123 <test>
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124 <param name="input1" value="1.bam" ftype="bam" />
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125 <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/>
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126 </test>
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127 <test>
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128 <param name="input1" value="1.bam" ftype="bam" />
2
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129 <conditional name="prim_key_cond">
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130 <param name="prim_key_select" value="-n"/>
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131 </conditional>
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132 <output name="output1" file="1_sort_read_names.bam" ftype="qname_sorted.bam"/>
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133 </test>
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134 </tests>
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135 <help>
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136 **What it does**
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137
2
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138 Sort alignments by leftmost coordinates, or by read name when -n is used.
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139 An appropriate @HD-SO sort order header tag will be added or an existing
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140 one updated if necessary.
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141
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142 **Ordering Rules**
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143
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144 The following rules are used for ordering records.
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145
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146 If option -t is in use, records are first sorted by the value of the given
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147 alignment tag, and then by position or name (if using -n). For example, “-t RG”
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148 will make read group the primary sort key. The rules for ordering by tag are:
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149
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150 - Records that do not have the tag are sorted before ones that do.
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151 - If the types of the tags are different, they will be sorted so that single
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152 character tags (type A) come before array tags (type B), then string tags
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153 (types H and Z), then numeric tags (types f and i).
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154 - Numeric tags (types f and i) are compared by value. Note that comparisons of
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155 floating-point values are subject to issues of rounding and precision.
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156 - String tags (types H and Z) are compared based on the binary contents of the
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157 tag using the C strcmp(3) function.
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158 - Character tags (type A) are compared by binary character value.
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159 - No attempt is made to compare tags of other types — notably type B array values will not be compared.
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160
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161 When the -n option is present, records are sorted by name. Names are compared so as to give a “natural” ordering — i.e. sections consisting of digits are compared numerically while all other sections are compared based on their binary representation. This means “a1” will come before “b1” and “a9” will come before “a10”. Records with the same name will be ordered according to the values of the READ1 and READ2 flags (see flags).
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162
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163 When the -n option is not present, reads are sorted by reference (according to the order of the @SQ header records), then by position in the reference, and then by the REVERSE flag.
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164
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165 This has now been removed. The previous out.prefix argument (and -f option, if any) should be changed to an appropriate combination of -T PREFIX and -o FILE. The previous -o option should be removed, as output defaults to standard output.
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166
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167 </help>
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cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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168 <expand macro="citations"/>
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169 </tool>