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annotate flash.xml @ 3:dce033fd3c80 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
author iuc
date Wed, 08 Nov 2017 11:06:11 -0500
parents b48895989d78
children c85bdba47254
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13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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1 <?xml version="1.0"?>
3
dce033fd3c80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
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2 <tool id="flash" name="FLASH" version="@VERSION@.3">
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3 <description>adjust length of short reads</description>
2
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4 <macros>
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5 <token name="@VERSION@">1.2.11</token>
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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6 </macros>
0
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7 <requirements>
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8 <requirement type="package" version="@VERSION@">flash</requirement>
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9 </requirements>
13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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10 <version_command>flash --version | head -n 1</version_command>
13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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11 <command detect_errors="aggressive">
13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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12 <![CDATA[
13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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13 flash --threads=\${GALAXY_SLOTS:-1}
13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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14 -m $min_overlap
13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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15 -M $max_overlap
13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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16 -x $max_mismatch_density
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17 $allow_outies
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18 #if $layout.select_layout == 'individual':
d043b54b3bfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
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19 '$layout.forward' '$layout.reverse'
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20 #set $input = $layout.forward
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21 #else:
d043b54b3bfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
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22 '$layout.reads.forward' '$layout.reads.reverse'
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23 #set $input = $layout.reads.forward
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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24 #end if
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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25 #if $input.dataset.extension == 'fastqsanger':
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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26 -p 33
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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27 #else:
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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28 -p 64
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29 #end if
3
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30
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31 #if $save_log:
dce033fd3c80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
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32 > '$log'
dce033fd3c80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
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33 #end if
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13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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34 ]]>
13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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35 </command>
13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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36 <inputs>
1
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37 <conditional name="layout">
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38 <param name="select_layout" type="select" label="Input data structure">
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39 <option value="individual">Individual datasets</option>
d043b54b3bfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
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40 <option value="collection">Paired collection</option>
d043b54b3bfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
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41 </param>
d043b54b3bfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
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42 <when value="individual">
2
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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43 <param format="fastqsanger,fastqsolexa,fastqillumina" name="forward" type="data" label="Forward reads" />
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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44 <param format="fastqsanger,fastqsolexa,fastqillumina" name="reverse" type="data" label="Reverse reads" />
1
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45 </when>
d043b54b3bfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
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46 <when value="collection">
2
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47 <param format="fastqsanger,fastqsolexa,fastqillumina" name="reads" type="data_collection" collection_type="paired" label="Paired reads" />
1
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48 </when>
d043b54b3bfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
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49 </conditional>
0
13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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50 <param name="min_overlap" argument="--min-overlap" type="integer" optional="true" value="10" label="Minimum overlap" help="The minimum required overlap length between two reads to provide a confident overlap." />
13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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51 <param name="max_overlap" argument="--max-overlap" type="integer" optional="true" value="65" label="Maximum overlap" help="Maximum overlap length expected in approximately 90% of read pairs. Overlaps longer than the maximum overlap parameter are still considered as good overlaps, but the mismatch density is calculated over the first max_overlap bases in the overlapped region rather than the entire overlap." />
13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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52 <param name="max_mismatch_density" argument="--max-mismatch-density" type="float" optional="true" value="0.25" label="Maximum mismatch density" help="Maximum allowed ratio between the number of mismatched base pairs and the overlap length. Two reads will not be combined with a given overlap if that overlap results in a mismatched base density higher than this value." />
13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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53 <param name="allow_outies" argument="--allow-outies" type="boolean" truevalue="--allow-outies" falsevalue="" checked="false" label="Combine read pairs in both orientations" help="FLASH uses the same parameters when trying each orientation. If a read pair can be combined in either orientation, the better-fitting one will be chosen using the same scoring algorithm that FLASH normally uses." />
1
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54 <param name="generate_histogram" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a text rendering of the histogram" />
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55 <param name="save_log" type="boolean" truevalue="" falsevalue="" checked="false" label="Save FLASH log file" />
0
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56 </inputs>
13e98e2709b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33
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57 <outputs>
2
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58 <data format_source="reads['forward']" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads">
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59 <filter>layout['select_layout'] == 'collection'</filter>
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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60 </data>
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61 <data format_source="reads['forward']" name="unmerged_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads">
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62 <filter>layout['select_layout'] == 'collection'</filter>
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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63 </data>
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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64 <data format_source="reads['reverse']" name="unmerged_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads">
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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65 <filter>layout['select_layout'] == 'collection'</filter>
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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66 </data>
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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67 <data format_source="forward" name="merged_paired_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads">
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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68 <filter>layout['select_layout'] == 'individual'</filter>
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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69 </data>
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70 <data format_source="forward" name="unmerged_paired_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads">
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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71 <filter>layout['select_layout'] == 'individual'</filter>
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72 </data>
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73 <data format_source="reverse" name="unmerged_paired_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads">
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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74 <filter>layout['select_layout'] == 'individual'</filter>
b48895989d78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
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75 </data>
0
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76 <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" />
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77 <data format="txt" name="log" label="${tool.name} on ${on_string}: Raw Log">
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78 <filter>raw_log == 'yes'</filter>
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79 </data>
1
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80 <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram">
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81 <filter>generate_histogram</filter>
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82 </data>
2
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83 <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)">
0
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84 <filter>allow_outies</filter>
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85 </data>
2
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86 <data format="tabular" name="hist_out" from_work_dir="out.hist.outie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (out)">
0
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87 <filter>allow_outies</filter>
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88 </data>
2
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89 <data format="txt" name="histogram_in" from_work_dir="out.histogram.innie" label="${tool.name} on ${on_string}: Unmerged reads histogram (in)">
1
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90 <filter>allow_outies and generate_histogram</filter>
0
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91 </data>
2
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92 <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)">
1
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93 <filter>allow_outies and generate_histogram</filter>
0
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94 </data>
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95 </outputs>
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96 <tests>
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97 <test>
2
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98 <param name="select_layout" value="individual" />
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99 <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" />
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100 <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" />
1
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101 <param name="generate_histogram" value="false" />
3
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102 <param name="save_log" value="true" />
2
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103 <output name="merged_paired_reads" file="flash_merged_out1.fastqsanger" ftype="fastqsanger" />
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104 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out1.fastqsanger" ftype="fastqsanger" />
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105 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out1.fastqsanger" ftype="fastqsanger" />
0
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106 <output name="hist" file="flash_hist_out1.tabular" />
3
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107 <output name="log">
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108 <assert_contents>
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109 <has_line_matching expression=".*Percent combined: 3.60%" />
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110 </assert_contents>
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111 </output>
0
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112 </test>
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113 <test>
2
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114 <param name="select_layout" value="individual" />
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115 <param name="forward" value="flash_forward_in2.fastqsanger" ftype="fastqsanger" />
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116 <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" />
0
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117 <param name="allow_outies" value="true" />
1
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118 <param name="generate_histogram" value="true" />
3
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119 <param name="save_log" value="true" />
2
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120 <output name="merged_paired_reads" file="flash_merged_out2.fastqsanger" ftype="fastqsanger" />
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121 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out2.fastqsanger" ftype="fastqsanger" />
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122 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out2.fastqsanger" ftype="fastqsanger" />
0
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123 <output name="hist" file="flash_hist_out2.tabular" />
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124 <output name="histogram" file="flash_hist_out2.txt" />
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125 <output name="hist_in" file="flash_hist_in_out2.tabular" />
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126 <output name="histogram_in" file="flash_hist_in_out2.txt" />
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127 <output name="hist_out" file="flash_hist_out_out2.tabular" />
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128 <output name="histogram_out" file="flash_hist_out_out2.txt" />
3
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129 <output name="log">
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130 <assert_contents>
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131 <has_line_matching expression=".*Percent combined: 3.80%" />
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132 </assert_contents>
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133 </output>
0
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134 </test>
2
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135 <test>
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136 <param name="select_layout" value="collection" />
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137 <param name="generate_histogram" value="false" />
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138 <param name="reads">
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139 <collection type="paired">
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140 <element name="forward" value="flash_forward_in3.fastqillumina" ftype="fastqillumina" />
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141 <element name="reverse" value="flash_reverse_in3.fastqillumina" ftype="fastqillumina" />
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142 </collection>
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143 </param>
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144 <output name="merged_reads" file="flash_merged_out3.fastqillumina" ftype="fastqillumina" />
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145 <output name="unmerged_reads_f" file="flash_unmerged_f_out3.fastqillumina" ftype="fastqillumina" />
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146 <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" />
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147 <output name="hist" file="flash_hist_out3.tabular" />
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148 </test>
0
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149 </tests>
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150 <help>
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151 <![CDATA[
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152 FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool
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153 to merge paired-end reads that were generated from DNA fragments whose
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154 lengths are shorter than twice the length of reads. Merged read pairs result
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155 in unpaired longer reads, which are generally more desired in genome
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156 assembly and genome analysis processes.
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157
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158 Briefly, the FLASH algorithm considers all possible overlaps at or above a
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159 minimum length between the reads in a pair and chooses the overlap that
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160 results in the lowest mismatch density (proportion of mismatched bases in
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161 the overlapped region). Ties between multiple overlaps are broken by
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162 considering quality scores at mismatch sites. When building the merged
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163 sequence, FLASH computes a consensus sequence in the overlapped region.
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164 ]]>
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165 </help>
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166 <citations>
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167 <citation type="doi">10.1093/bioinformatics/btr507</citation>
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168 </citations>
2
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169 </tool>