Mercurial > repos > rnateam > mirdeep2_mapper
annotate mapper.xml @ 2:f844a9c1698d draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
| author | rnateam |
|---|---|
| date | Wed, 23 Nov 2016 16:01:29 -0500 |
| parents | bda96b97c289 |
| children | 79fdac89dd6e |
| rev | line source |
|---|---|
| 0 | 1 <tool id="rbc_mirdeep2_mapper" name="MiRDeep2 Mapper" version="2.0.0"> |
| 2 <macros> | |
| 3 <macro name="map_params"> | |
| 4 <conditional name="refGenomeSource"> | |
| 5 <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)"> | |
| 6 <option value="indexed">Use a built-in index</option> | |
| 7 <option value="history">Use one from the history</option> | |
| 8 </param> | |
| 9 <when value="indexed"> | |
| 10 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin."> | |
| 11 <options from_data_table="bowtie_indexes"> | |
| 12 <filter type="sort_by" column="2"/> | |
| 13 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | |
| 14 </options> | |
| 15 </param> | |
| 16 </when> <!-- build-in --> | |
| 17 <when value="history"> | |
| 18 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> | |
| 19 </when> <!-- history --> | |
| 20 </conditional> <!-- refGenomeSource --> | |
| 21 <param name="map_mismatch" type="boolean" truevalue="-q" falsevalue="" checked="false" label="Map with one mismatch in the seed (mapping takes longer)" help="(-q)"/> | |
| 22 <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)"> | |
| 23 <validator type="in_range" min="1" message="Minimum value is 1"/> | |
| 24 </param> | |
| 25 </macro> | |
| 26 </macros> | |
| 27 <description> | |
| 28 <![CDATA[ | |
| 29 process and map reads to a reference genome | |
| 30 ]]> | |
| 31 </description> | |
| 32 <requirements> | |
| 33 <requirement type="package" version="2.0">mirdeep2_mapper</requirement> | |
| 34 <requirement type="package" version="0.12.7">bowtie</requirement> | |
| 35 <requirement type="package" version="5.18.1">perl</requirement> | |
| 36 </requirements> | |
| 37 | |
| 38 <command> | |
| 39 <![CDATA[ | |
| 40 | |
| 41 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map" | |
| 42 #if $operation.refGenomeSource.genomeSource == "history" | |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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43 bowtie-build '$operation.refGenomeSource.ownFile' custom_bowtie_indices && |
| 0 | 44 #end if |
| 45 #end if | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
rnateam
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46 |
| 0 | 47 mapper.pl |
| 48 | |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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49 '$reads' |
| 0 | 50 |
| 51 #if $reads.extension.startswith("fasta") | |
| 52 -c | |
| 53 #else if $reads.extension.startswith("fastq") | |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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54 -e |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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55 -h |
| 0 | 56 #end if |
| 57 | |
| 58 $remove_non_canon | |
| 59 | |
| 60 $convert_rna_dna | |
| 61 | |
| 62 #if $clip_adapter.clip == "true" | |
| 63 -k $clip_adapter.adapter_seq | |
| 64 #end if | |
| 65 | |
| 66 -l $discard_short_reads | |
| 67 | |
| 68 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_collapse" | |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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69 -m -s '$output_reads_collapsed' |
| 0 | 70 #end if |
| 71 | |
| 72 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map" | |
| 73 -p | |
| 74 | |
| 75 #if $operation.refGenomeSource.genomeSource == "history" | |
| 76 custom_bowtie_indices | |
| 77 #else | |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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78 '$operation.refGenomeSource.index.fields.path' |
| 0 | 79 #end if |
| 80 $operation.map_mismatch | |
| 81 -r $operation.map_threshold | |
| 82 | |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
rnateam
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83 -t '$output_mapping' |
| 0 | 84 #end if |
| 85 | |
| 86 -v -n | |
| 87 ]]> | |
| 88 </command> | |
| 89 <stdio> | |
| 90 <!-- Anything other than zero is an error --> | |
| 91 <exit_code range="1:" /> | |
| 92 <exit_code range=":-1" /> | |
| 93 <!-- In case the return code has not been set propery check stderr too --> | |
| 94 <regex match="Error:" /> | |
| 95 <regex match="Exception:" /> | |
| 96 </stdio> | |
| 97 <inputs> | |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
rnateam
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98 <param format="fastq, fasta" name="reads" type="data" optional="false" label="Deep sequencing reads" help="Reads in fastq or FASTA format"/> |
| 0 | 99 <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)"/> |
| 100 <param name="convert_rna_dna" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Convert RNA to DNA alphabet (to map against genome)" help="(-i)"/> | |
| 101 | |
| 102 <conditional name="clip_adapter"> | |
| 103 <param name="clip" type="select" label="Clip 3' Adapter Sequence" help="(-k)"> | |
| 104 <option value="false">Don't Clip</option> | |
| 105 <option value="true">Clip Sequence</option> | |
| 106 </param> | |
| 107 <when value="true"> | |
| 108 <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"> | |
| 109 <validator type="regex" message="Adapter can ONLY contain a,c,g,t,u,n,A,C,G,T,U,N">^[ACGTUacgtu]+$</validator> | |
| 110 </param> | |
| 111 </when> | |
| 112 <when value="false"/> | |
| 113 </conditional> | |
| 114 | |
| 115 <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)"> | |
| 116 <validator type="in_range" min="0" message="Minimum value is 0"/> | |
| 117 </param> | |
| 118 | |
| 119 <conditional name="operation"> | |
| 120 <param name="collapse_map" type="select" label="Collapse reads and/or Map" help="(-m) and/or (-p)"> | |
| 121 <option value="collapse_and_map">Collapse reads and Map</option> | |
| 122 <option value="only_map">Map</option> | |
| 123 <option value="only_collapse">Collapse</option> | |
| 124 </param> | |
| 125 <when value="collapse_and_map"> | |
| 126 <expand macro="map_params"/> | |
| 127 </when> | |
| 128 <when value="only_map"> | |
| 129 <expand macro="map_params"/> | |
| 130 </when> | |
| 131 <when value="only_collapse"/> | |
| 132 </conditional> | |
| 133 </inputs> | |
| 134 <outputs> | |
| 135 <data format="fasta" name="output_reads_collapsed" label="Collapsed reads of ${tool.name} on ${on_string}"> | |
| 136 <filter> | |
| 137 ( | |
| 138 operation['collapse_map'] == "collapse_and_map" or | |
| 139 operation['collapse_map'] == "only_collapse" | |
| 140 ) | |
| 141 </filter> | |
| 142 </data> | |
| 143 <data format="tabular" name="output_mapping" label="Mapping output of ${tool.name} on ${on_string} in ARF format"> | |
| 144 <filter> | |
| 145 ( | |
| 146 operation['collapse_map'] == "collapse_and_map" or | |
| 147 operation['collapse_map'] == "only_map" | |
| 148 ) | |
| 149 </filter> | |
| 150 </data> | |
| 151 </outputs> | |
| 152 <tests> | |
| 153 <test> | |
| 154 <param name="reads" value="reads.fa"/> | |
| 155 <param name="remove_non_canon" value="True"/> | |
| 156 <param name="clip" value="true"/> | |
| 157 <param name="adapter_seq" value="TCGTATGCCGTCTTCTGCTTGT"/> | |
| 158 <param name="discard_short_reads" value="18"/> | |
| 159 <param name="collapse_map" value="collapse_and_map"/> | |
| 160 <param name="genomeSource" value="history"/> | |
| 161 <param name="ownFile" value="cel_cluster.fa"/> | |
| 162 <output name="output_reads_collapsed"> | |
| 163 <assert_contents> | |
| 164 <has_text text=">seq_349713_x268"/> | |
| 165 <has_text text="TCACCGGGTGTANATCAGCTAA"/> | |
| 166 <has_text text=">seq_354255_x214"/> | |
| 167 <has_text text="TAACCGGGTGAACACTTGCAGT"/> | |
| 168 <has_text text=">seq_357284_x187"/> | |
| 169 </assert_contents> | |
| 170 </output> | |
| 171 <output name="output_mapping"> | |
| 172 <assert_contents> | |
| 173 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtggaaactagcagt\tchrII:11534525-11540624\t22\t3060\t3081.*$"/> | |
| 174 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtggaaactagtagt\tchrII:11534525-11540624\t22\t3060\t3081.*$"/> | |
| 175 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtgtacatcagcgaa\tchrII:11534525-11540624\t22\t3631\t3652.*$"/> | |
| 176 <has_line_matching expression="^.*22\t1\t22\ttcaccgggagaaaaactggtgt\tchrII:11534525-11540624\t22\t3382\t3403.*$"/> | |
| 177 <has_line_matching expression="^.*25\t1\t25\ttcaccgggtggaaactagcagtggc\tchrII:11534525-11540624\t25\t3060\t3084.*$"/> | |
| 178 </assert_contents> | |
| 179 </output> | |
| 180 </test> | |
| 181 </tests> | |
| 182 <help> | |
| 183 <![CDATA[ | |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
rnateam
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184 **What it does** |
| 0 | 185 |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
rnateam
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186 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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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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187 The module works in sequence space, and can process or map data that is in sequence FASTA format. |
| 0 | 188 A number of the functions of the mapper module are implemented specifically with Solexa/Illumina data in mind. |
| 189 | |
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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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190 **Input** |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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191 |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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192 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 | 193 |
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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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194 **Output** |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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195 |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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196 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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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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197 |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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198 Arf format: |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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199 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 | 200 |
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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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201 1. read identifier |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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202 2. length of read sequence |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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203 3. start position in read sequence that is mapped |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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204 4. end position in read sequence that is mapped |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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205 5. read sequence |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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206 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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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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207 7. length of the genome sequence a read is mapped to |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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208 8. start position in the genome where a read is mapped to |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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209 9. end position in the genome where a read is mapped to |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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210 10. genome sequence to which a read is mapped |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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211 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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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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212 12. Number of mismatches in the read mapping |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
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213 13. Edit string that indicates matches by lowercase 'm' and mismatches by uppercase 'M' |
| 0 | 214 |
| 215 ]]> | |
| 216 </help> | |
| 217 <citations> | |
| 218 <citation type="doi">10.1093/nar/gkr688</citation> | |
| 219 <citation type="doi">10.1002/0471250953.bi1210s36</citation> | |
| 220 </citations> | |
| 221 </tool> |