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comparison sRbowtie.xml @ 1:b50d7228b678 draft

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author mvdbeek
date Sun, 29 Mar 2015 10:25:36 -0400
parents 64064dccdb11
children 316124e85b8d
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0:64064dccdb11 1:b50d7228b678
1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.0"> 1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.0">
2 <description>for FASTA small reads</description> 2 <description>for FASTA small reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.12.7">bowtie</requirement> 4 <requirement type="package" version="0.12.7">bowtie</requirement>
5 <requirement type="package" version="0.1.18">samtools</requirement> 5 <requirement type="package" version="0.1.18">samtools</requirement>
6 </requirements> 6 </requirements>
7 <parallelism method="basic"></parallelism> 7 <command interpreter="python"> sRbowtie.py --input $input
8 <command interpreter="python"> sRbowtie.py --input $input 8 --input-format $input.extension
9 --method $method 9 --method $method
10 --v-mismatches $v_mismatches 10 --v-mismatches $v_mismatches
11 --output-format $output_format 11 --output-format $output_format
12 --output $output 12 --output $output
13 --index-from $refGenomeSource.genomeSource 13 --index-from $refGenomeSource.genomeSource
20 #end if 20 #end if
21 --aligned $aligned 21 --aligned $aligned
22 --unaligned $unaligned 22 --unaligned $unaligned
23 --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie 23 --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
24 </command> 24 </command>
25 <inputs> 25 <inputs>
26 <param name="input" type="data" format="fasta" label="Input fasta file: reads clipped from their adapter" help="Only with clipped, raw fasta files"/> 26 <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" />
27 <!-- which method will be used --> 27 <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select">
28 <param name="method" type="select" label="What kind of matching do you want to do?" help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand"> 28 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
29 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option> 29 <option value="unique">Match unique mappers on DNA reference index</option>
30 <option value="unique">Match unique mappers on DNA reference index</option> 30 <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option>
31 <option value="multiple" selected="true">Match on DNA, multiple mappers randomly matched at a single position</option> 31 <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option>
32 <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option> 32 <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option>
33 <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option> 33 <option value="a_option">Match and report all valid alignments</option>
34 <option value="a_option">Match and report all valid alignments</option> 34 </param>
35 </param> 35 <param help="specify the -v bowtie option" label="Number of mismatches allowed" name="v_mismatches" type="select">
36 <!-- END of which method will be used --> 36 <option value="0">0</option>
37 <param name="v_mismatches" type="select" label="Number of mismatches allowed" help="specify the -v bowtie option"> 37 <option selected="true" value="1">1</option>
38 <option value="0">0</option> 38 <option value="2">2</option>
39 <option value="1" selected="true">1</option> 39 <option value="3">3</option>
40 <option value="2">2</option> 40 </param>
41 <option value="3">3</option> 41 <conditional name="refGenomeSource">
42 </param> 42 <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select">
43 <!-- bowtie index selection --> 43 <option value="indexed">Use a built-in index</option>
44 <conditional name="refGenomeSource"> 44 <option value="history">Use one from the history</option>
45 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> 45 </param>
46 <option value="indexed">Use a built-in index</option> 46 <when value="indexed">
47 <option value="history">Use one from the history</option> 47 <param help="if your genome of interest is not listed - contact GED team" label="Select a DNA reference index" name="index" type="select">
48 </param> 48 <options from_data_table="bowtie_indexes">
49 <when value="indexed"> 49
50 <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact GED team">
51 <options from_data_table="bowtie_indexes">
52 <!-- <filter type="sort_by" column="2" />
53 <validator type="no_options" message="No indexes are available" /> -->
54 </options> 50 </options>
55 </param> 51 </param>
56 </when> 52 </when>
57 <when value="history"> 53 <when value="history">
58 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" /> 54 <param format="fasta" label="Select a fasta file, to serve as index reference" name="ownFile" type="data" />
59 </when> 55 </when>
60 </conditional>
61 <!-- END bowtie index selection -->
62 <param name="output_format" type="select" label="Select output format" help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below">
63 <option value="tabular" select="true">tabular</option>
64 <option value="sam">sam</option>
65 <option value="bam">bam</option>
66 </param>
67 <param name="additional_fasta" type="select" label="additional fasta output" help="to get aligned and unaligned reads in fasta format">
68 <option value="No" select="true">No</option>
69 <option value="al">aligned</option>
70 <option value="unal">unaligned</option>
71 <option value="al_and_unal">both aligned and unaligned</option>
72 </param>
73 </inputs>
74 <outputs>
75 <data format="tabular" name="output" label="Bowtie Output">
76 <change_format>
77 <when input="output_format" value="sam" format="sam" />
78 <when input="output_format" value="bam" format="bam" />
79 </change_format>
80 <!-- Set metadata based on reference genome -->
81 <actions>
82 <conditional name="refGenomeSource.genomeSource">
83 <when value="indexed">
84 <action type="metadata" name="dbkey">
85 <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">
86 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
87 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
88 </option>
89 </action>
90 </when>
91 <when value="history">
92 <action type="metadata" name="dbkey">
93 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
94 </action>
95 </when>
96 </conditional> 56 </conditional>
97 </actions> 57 <param help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below" label="Select output format" name="output_format" type="select">
98 </data> 58 <option select="true" value="tabular">tabular</option>
99 <data format="fasta" name="aligned" label="Matched reads"> 59 <option value="sam">sam</option>
100 <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter> 60 <option value="bam">bam</option>
101 </data> 61 </param>
102 <data format="fasta" name="unaligned" label ="Unmatched reads"> 62 <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select">
103 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter> 63 <option select="true" value="No">No</option>
104 </data> 64 <option value="al">aligned</option>
105 </outputs> 65 <option value="unal">unaligned</option>
106 66 <option value="al_and_unal">both aligned and unaligned</option>
107 <test> 67 </param>
108 <param name="genomeSource" value="indexed" /> 68 </inputs>
109 <param name="index" value="/home/galaxy/galaxy-dist/bowtie/Dmel/dmel-all-chromosome-r5.49" /> 69 <outputs>
110 <param name="method" value="multiple" /> 70 <data format="tabular" label="Bowtie Output" name="output">
111 <param name="input" ftype="fasta" value="sRbowtie.fa" /> 71 <change_format>
112 <param name="v_mismatches" value="1" /> 72 <when format="sam" input="output_format" value="sam" />
113 <param name="output_format" value="tabular" /> 73 <when format="bam" input="output_format" value="bam" />
114 <output name="output" ftype="tabular" value="sRbowtie.out" /> 74 </change_format>
115 <output name="aligned" value="None" /> 75 <actions>
116 <output name="unaligned" value="None" /> 76 <conditional name="refGenomeSource.genomeSource">
117 </test> 77 <when value="indexed">
118 78 <action name="dbkey" type="metadata">
119 <help> 79 <option column="1" name="bowtie_indexes" offset="0" type="from_data_table">
80 <filter column="0" compare="startswith" keep="False" type="param_value" value="#" />
81 <filter column="0" ref="refGenomeSource.index" type="param_value" />
82 </option>
83 </action>
84 </when>
85 <when value="history">
86 <action name="dbkey" type="metadata">
87 <option name="refGenomeSource.ownFile" param_attribute="dbkey" type="from_param" />
88 </action>
89 </when>
90 </conditional>
91 </actions>
92 </data>
93 <data format="fasta" label="Matched reads" name="aligned">
94 <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter>
95 </data>
96 <data format="fasta" label="Unmatched reads" name="unaligned">
97 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter>
98 </data>
99 </outputs>
100 <tests>
101 <test>
102 <param name="genomeSource" value="history" />
103 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
104 <param name="method" value="unique" />
105 <param ftype="fasta" name="input" value="input.fa" />
106 <param name="v_mismatches" value="1" />
107 <param name="output_format" value="bam" />
108 <output file="output.bam" ftype="bam" lines_diff="4" name="output" />
109 </test>
110 <test>
111 <param name="genomeSource" value="history" />
112 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
113 <param name="method" value="unique" />
114 <param ftype="fastq" name="input" value="input.fastq" />
115 <param name="v_mismatches" value="1" />
116 <param name="output_format" value="bam" />
117 <output file="output2.bam" ftype="bam" lines_diff="4" name="output" />
118 </test>
119 </tests>
120 <help>
120 121
121 **What it does** 122 **What it does**
122 123
123 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25. 124 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
124 125
207 Please contact the Galaxy instance administrator if your genome is not referenced 208 Please contact the Galaxy instance administrator if your genome is not referenced
208 209
209 **Matched and unmatched fasta reads can be retrieved, for further analyses** 210 **Matched and unmatched fasta reads can be retrieved, for further analyses**
210 211
211 </help> 212 </help>
213 <citations>
214 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
215 </citations>
212 </tool> 216 </tool>