Mercurial > repos > rnateam > mirdeep2_mapper
annotate mapper.xml @ 3:a8d24f4b6d95 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
| author | rnateam |
|---|---|
| date | Wed, 12 Jul 2017 14:38:46 -0400 |
| parents | ab8cd78709e1 |
| children | dbbe92348c7a |
| rev | line source |
|---|---|
| 0 | 1 <tool id="rbc_mirdeep2_mapper" name="MiRDeep2 Mapper" version="2.0.0"> |
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a8d24f4b6d95
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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2 <description>process and map reads to a reference genome</description> |
| 0 | 3 <macros> |
| 4 <macro name="map_params"> | |
| 5 <conditional name="refGenomeSource"> | |
| 6 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Map to genome. (-p)"> | |
| 7 <option value="indexed">Use a built-in index</option> | |
| 8 <option value="history">Use one from the history</option> | |
| 9 </param> | |
| 10 <when value="indexed"> | |
| 11 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin."> | |
| 12 <options from_data_table="bowtie_indexes"> | |
| 13 <filter type="sort_by" column="2"/> | |
| 14 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | |
| 15 </options> | |
| 16 </param> | |
| 17 </when> <!-- build-in --> | |
| 18 <when value="history"> | |
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a8d24f4b6d95
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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19 <param name="ownFile" type="data" format="fasta" label="Select the reference genome" /> |
| 0 | 20 </when> <!-- history --> |
| 21 </conditional> <!-- refGenomeSource --> | |
| 22 <param name="map_mismatch" type="boolean" truevalue="-q" falsevalue="" checked="false" label="Map with one mismatch in the seed (mapping takes longer)" help="(-q)"/> | |
| 23 <param name="map_threshold" value="5" type="integer" optional="false" label="A read is allowed to map up to this number of positions in the genome" help="Map threshold. (-r)"> | |
| 24 <validator type="in_range" min="1" message="Minimum value is 1"/> | |
| 25 </param> | |
| 26 </macro> | |
| 27 </macros> | |
| 28 <requirements> | |
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a8d24f4b6d95
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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29 <requirement type="package" version="2.0.0.8">mirdeep2</requirement> |
| 0 | 30 </requirements> |
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a8d24f4b6d95
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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31 <stdio> |
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a8d24f4b6d95
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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32 <!-- Anything other than zero is an error --> |
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a8d24f4b6d95
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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33 <exit_code range="1:" /> |
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a8d24f4b6d95
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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34 <exit_code range=":-1" /> |
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a8d24f4b6d95
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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35 <!-- In case the return code has not been set propery check stderr too --> |
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a8d24f4b6d95
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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36 <regex match="Error:" /> |
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a8d24f4b6d95
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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changeset
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37 <regex match="Exception:" /> |
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a8d24f4b6d95
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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38 </stdio> |
| 0 | 39 <command> |
| 40 <![CDATA[ | |
| 41 | |
| 42 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map" | |
| 43 #if $operation.refGenomeSource.genomeSource == "history" | |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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44 bowtie-build '$operation.refGenomeSource.ownFile' custom_bowtie_indices && |
| 0 | 45 #end if |
| 46 #end if | |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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47 |
| 0 | 48 mapper.pl |
| 49 | |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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50 '$reads' |
| 0 | 51 |
| 52 #if $reads.extension.startswith("fasta") | |
| 53 -c | |
| 54 #else if $reads.extension.startswith("fastq") | |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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55 -e |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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56 -h |
| 0 | 57 #end if |
| 58 | |
| 59 $remove_non_canon | |
| 60 | |
| 61 $convert_rna_dna | |
| 62 | |
| 63 #if $clip_adapter.clip == "true" | |
| 64 -k $clip_adapter.adapter_seq | |
| 65 #end if | |
| 66 | |
| 67 -l $discard_short_reads | |
| 68 | |
| 69 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_collapse" | |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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70 -m -s '$output_reads_collapsed' |
| 0 | 71 #end if |
| 72 | |
| 73 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map" | |
| 74 -p | |
| 75 | |
| 76 #if $operation.refGenomeSource.genomeSource == "history" | |
| 77 custom_bowtie_indices | |
| 78 #else | |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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79 '$operation.refGenomeSource.index.fields.path' |
| 0 | 80 #end if |
| 81 $operation.map_mismatch | |
| 82 -r $operation.map_threshold | |
| 83 | |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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84 -t '$output_mapping' |
| 0 | 85 #end if |
| 86 | |
| 87 -v -n | |
| 88 ]]> | |
| 89 </command> | |
| 90 <inputs> | |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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91 <param format="fastq, fasta" name="reads" type="data" optional="false" label="Deep sequencing reads" help="Reads in fastq or FASTA format"/> |
| 0 | 92 <param name="remove_non_canon" type="boolean" truevalue="-j" falsevalue="" checked="false" label="Remove reads with non-standard nucleotides" help="Remove all entries that have a sequence that contains letters other than a,c,g,t,u,n,A,C,G,T,U,N. (-j)"/> |
| 93 <param name="convert_rna_dna" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Convert RNA to DNA alphabet (to map against genome)" help="(-i)"/> | |
| 94 | |
| 95 <conditional name="clip_adapter"> | |
| 96 <param name="clip" type="select" label="Clip 3' Adapter Sequence" help="(-k)"> | |
| 97 <option value="false">Don't Clip</option> | |
| 98 <option value="true">Clip Sequence</option> | |
| 99 </param> | |
| 100 <when value="true"> | |
| 101 <param name="adapter_seq" value="" type="text" optional="false" label="Sequence to clip" help="Adapter Sequence can only contain a,c,g,t,u,n,A,C,G,T,U,N"> | |
| 102 <validator type="regex" message="Adapter can ONLY contain a,c,g,t,u,n,A,C,G,T,U,N">^[ACGTUacgtu]+$</validator> | |
| 103 </param> | |
| 104 </when> | |
| 105 <when value="false"/> | |
| 106 </conditional> | |
| 107 | |
| 108 <param name="discard_short_reads" value="18" type="integer" optional="false" label="Discard reads shorter than this length" help="Set to 0 to keep all reads. (-l)"> | |
| 109 <validator type="in_range" min="0" message="Minimum value is 0"/> | |
| 110 </param> | |
| 111 | |
| 112 <conditional name="operation"> | |
| 113 <param name="collapse_map" type="select" label="Collapse reads and/or Map" help="(-m) and/or (-p)"> | |
| 114 <option value="collapse_and_map">Collapse reads and Map</option> | |
| 115 <option value="only_map">Map</option> | |
| 116 <option value="only_collapse">Collapse</option> | |
| 117 </param> | |
| 118 <when value="collapse_and_map"> | |
| 119 <expand macro="map_params"/> | |
| 120 </when> | |
| 121 <when value="only_map"> | |
| 122 <expand macro="map_params"/> | |
| 123 </when> | |
| 124 <when value="only_collapse"/> | |
| 125 </conditional> | |
| 126 </inputs> | |
| 127 <outputs> | |
| 128 <data format="fasta" name="output_reads_collapsed" label="Collapsed reads of ${tool.name} on ${on_string}"> | |
| 129 <filter> | |
| 130 ( | |
| 131 operation['collapse_map'] == "collapse_and_map" or | |
| 132 operation['collapse_map'] == "only_collapse" | |
| 133 ) | |
| 134 </filter> | |
| 135 </data> | |
| 136 <data format="tabular" name="output_mapping" label="Mapping output of ${tool.name} on ${on_string} in ARF format"> | |
| 137 <filter> | |
| 138 ( | |
| 139 operation['collapse_map'] == "collapse_and_map" or | |
| 140 operation['collapse_map'] == "only_map" | |
| 141 ) | |
| 142 </filter> | |
| 143 </data> | |
| 144 </outputs> | |
| 145 <tests> | |
| 146 <test> | |
| 147 <param name="reads" value="reads.fa"/> | |
| 148 <param name="remove_non_canon" value="True"/> | |
| 149 <param name="clip" value="true"/> | |
| 150 <param name="adapter_seq" value="TCGTATGCCGTCTTCTGCTTGT"/> | |
| 151 <param name="discard_short_reads" value="18"/> | |
| 152 <param name="collapse_map" value="collapse_and_map"/> | |
| 153 <param name="genomeSource" value="history"/> | |
| 154 <param name="ownFile" value="cel_cluster.fa"/> | |
| 155 <output name="output_reads_collapsed"> | |
| 156 <assert_contents> | |
| 157 <has_text text=">seq_349713_x268"/> | |
| 158 <has_text text="TCACCGGGTGTANATCAGCTAA"/> | |
| 159 <has_text text=">seq_354255_x214"/> | |
| 160 <has_text text="TAACCGGGTGAACACTTGCAGT"/> | |
| 161 <has_text text=">seq_357284_x187"/> | |
| 162 </assert_contents> | |
| 163 </output> | |
| 164 <output name="output_mapping"> | |
| 165 <assert_contents> | |
| 166 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtggaaactagcagt\tchrII:11534525-11540624\t22\t3060\t3081.*$"/> | |
| 167 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtggaaactagtagt\tchrII:11534525-11540624\t22\t3060\t3081.*$"/> | |
| 168 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtgtacatcagcgaa\tchrII:11534525-11540624\t22\t3631\t3652.*$"/> | |
| 169 <has_line_matching expression="^.*22\t1\t22\ttcaccgggagaaaaactggtgt\tchrII:11534525-11540624\t22\t3382\t3403.*$"/> | |
| 170 <has_line_matching expression="^.*25\t1\t25\ttcaccgggtggaaactagcagtggc\tchrII:11534525-11540624\t25\t3060\t3084.*$"/> | |
| 171 </assert_contents> | |
| 172 </output> | |
| 173 </test> | |
| 174 </tests> | |
| 175 <help> | |
| 176 <![CDATA[ | |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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177 **What it does** |
| 0 | 178 |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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179 The MiRDeep2 Mapper module is designed as a tool to process deep sequencing reads and/or map them to the reference genome. |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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180 The module works in sequence space, and can process or map data that is in sequence FASTA format. |
| 0 | 181 A number of the functions of the mapper module are implemented specifically with Solexa/Illumina data in mind. |
| 182 | |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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183 **Input** |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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184 |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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185 Default input is a file in FASTA format, seq.txt or qseq.txt format. More input can be given depending on the options used. |
| 0 | 186 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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187 **Output** |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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188 |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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189 The output depends on the options used. Either a FASTA file with processed reads or an arf file with with mapped reads, or both, are output. |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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190 |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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191 Arf format: |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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192 Is a proprietary file format generated and processed by miRDeep2. It contains information of reads mapped to a reference genome. Each line in such a file contains 13 columns: |
| 0 | 193 |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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194 1. read identifier |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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195 2. length of read sequence |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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196 3. start position in read sequence that is mapped |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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197 4. end position in read sequence that is mapped |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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198 5. read sequence |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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199 6. identifier of the genome-part to which a read is mapped to. This is either a scaffold id or a chromosome name |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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200 7. length of the genome sequence a read is mapped to |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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201 8. start position in the genome where a read is mapped to |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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202 9. end position in the genome where a read is mapped to |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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203 10. genome sequence to which a read is mapped |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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204 11. genome strand information. Plus means the read is aligned to the sense-strand of the genome. Minus means it is aligned to the antisense-strand of the genome. |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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205 12. Number of mismatches in the read mapping |
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ab8cd78709e1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
rnateam
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206 13. Edit string that indicates matches by lowercase 'm' and mismatches by uppercase 'M' |
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| 208 ]]> | |
| 209 </help> | |
| 210 <citations> | |
| 211 <citation type="doi">10.1093/nar/gkr688</citation> | |
| 212 <citation type="doi">10.1002/0471250953.bi1210s36</citation> | |
| 213 </citations> | |
| 214 </tool> |