Mercurial > repos > peterjc > clc_assembly_cell
annotate tools/clc_assembly_cell/clc_assembler.xml @ 5:31a9169b6222 draft default tip
"Update all the pico_galaxy tools on main Tool Shed"
| author | peterjc |
|---|---|
| date | Fri, 16 Apr 2021 22:32:53 +0000 |
| parents | 46a667b5e19e |
| children |
| rev | line source |
|---|---|
| 5 | 1 <tool id="clc_assembler" name="CLC assembler" version="0.0.7"> |
| 0 | 2 <description>Assembles reads giving a FASTA file</description> |
| 5 | 3 <version_command> |
| 4 ${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version | |
| 5 </version_command> | |
| 6 <command detect_errors="aggressive"> | |
| 7 \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | |
| 0 | 8 #for $rg in $read_group |
| 9 ##-------------------------------------- | |
| 10 #if str($rg.segments.type) == "paired" | |
| 11 -p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i "$rg.segments.filename1" "$rg.segments.filename2" | |
| 12 #end if | |
| 13 ##-------------------------------------- | |
| 14 #if str($rg.segments.type) == "interleaved" | |
| 15 -p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q "$rg.segments.filename" | |
| 16 #end if | |
| 17 ##-------------------------------------- | |
| 18 #if str($rg.segments.type) == "none" | |
| 19 -p no -q | |
| 20 #for $f in $rg.segments.filenames | |
| 21 "$f" | |
| 22 #end for | |
| 23 #end if | |
| 24 ##-------------------------------------- | |
| 25 #end for | |
| 26 -m $min_contig_len | |
| 27 -o "$out_fasta" | |
| 28 --cpus \${GALAXY_SLOTS:-4} | |
| 29 -v | grep -v "^Progress: "</command> | |
| 30 <inputs> | |
| 31 <repeat name="read_group" title="Read Group" min="1"> | |
| 32 <conditional name="segments"> | |
| 33 <param name="type" type="select" label="Are these paired reads?"> | |
| 34 <option value="paired">Paired reads (as two files)</option> | |
| 35 <option value="interleaved">Paired reads (as one interleaved file)</option> | |
| 36 <option value="none">Unpaired reads (single or orphan reads)</option> | |
| 37 </param> | |
| 38 <when value="paired"> | |
| 39 <param name="placement" type="select" label="Pairing type (segment placing)"> | |
| 40 <option value="fb">---> <--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option> | |
| 41 <option value="bf"><--- ---> (e.g. Solexa/Illumina mate-pair library)</option> | |
| 42 <option value="ff">---> ---></option> | |
| 43 <option value="bb"><--- <---</option> | |
| 44 </param> | |
| 45 <param name="dist_mode" type="select" label="How is the fragment distance measured?"> | |
| 46 <option value="ss">Start to start (e.g. Sanger capillary or Solexa/Illumina libraries)</option> | |
| 47 <option value="se">Start to end</option> | |
| 48 <option value="es">End to start</option> | |
| 49 <option value="ee">End to end</option> | |
| 50 </param> | |
| 51 <!-- TODO - min/max validation done via the <code> tag? --> | |
| 52 <param name="min_size" type="integer" optional="false" min="0" value="" | |
| 53 label="Minimum size of 'good' DNA templates in the library preparation" /> | |
| 54 <param name="max_size" type="integer" optional="false" min="0" value="" | |
| 55 label="Maximum size of 'good' DNA templates in the library preparation" /> | |
|
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46a667b5e19e
v0.0.6 update optional/required parameters and URLS in docs
peterjc
parents:
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diff
changeset
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56 <param name="filename1" type="data" format="fastq,fasta" label="Read file one"/> |
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46a667b5e19e
v0.0.6 update optional/required parameters and URLS in docs
peterjc
parents:
2
diff
changeset
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57 <param name="filename2" type="data" format="fastq,fasta" label="Read file two"/> |
| 0 | 58 </when> |
| 59 <when value="interleaved"> | |
| 60 <param name="placement" type="select" label="Pairing type (segment placing)"> | |
| 61 <option value="fb">---> <--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option> | |
| 62 <option value="bf"><--- ---> (e.g. Solexa/Illumina mate-pair library)</option> | |
| 63 <option value="ff">---> ---></option> | |
| 64 <option value="bb"><-- <--</option> | |
| 65 </param> | |
| 66 <param name="dist_mode" type="select" label="How is the fragment distance measured?"> | |
| 67 <option value="ss">Start to start (e.g. Sanger capillary or Solexa/Illumina libraries)</option> | |
| 68 <option value="se">Start to end</option> | |
| 69 <option value="es">End to start</option> | |
| 70 <option value="ee">End to end</option> | |
| 71 </param> | |
| 72 <!-- TODO - min/max validation done via the <code> tag? --> | |
| 73 <param name="min_size" type="integer" optional="false" min="0" value="" | |
| 74 label="Minimum size of 'good' DNA templates in the library preparation" /> | |
| 75 <param name="max_size" type="integer" optional="false" min="0" value="" | |
| 76 label="Maximum size of 'good' DNA templates in the library preparation" /> | |
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46a667b5e19e
v0.0.6 update optional/required parameters and URLS in docs
peterjc
parents:
2
diff
changeset
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77 <param name="filename" type="data" format="fastq,fasta" label="Interleaved read file"/> |
| 0 | 78 </when> |
| 79 <when value="none"> | |
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46a667b5e19e
v0.0.6 update optional/required parameters and URLS in docs
peterjc
parents:
2
diff
changeset
|
80 <param name="filenames" type="data" format="fastq,fasta" multiple="true" optional="false" label="Read file(s)" |
| 0 | 81 help="Multiple files allowed, for example several files of orphan reads." /> |
| 82 </when> | |
| 83 </conditional> | |
| 84 </repeat> | |
| 85 <param name="min_contig_len" type="integer" optional="false" min="1" value="200" label="Minimum contig length"/> | |
| 86 <!-- Word size? --> | |
| 87 <!-- Bubble size? --> | |
| 88 <!-- Scaffolding options? --> | |
| 89 <!-- AGP / GFF output? --> | |
| 90 </inputs> | |
| 91 <!-- min/max validation? <code file="clc_validator.py" /> --> | |
| 92 <outputs> | |
| 93 <data name="out_fasta" format="fasta" label="CLCbio assember contigs (FASTA)" /> | |
| 94 </outputs> | |
| 95 <tests> | |
| 96 <test> | |
| 97 <param name="read_group_0|segments|type" value="interleaved" /> | |
| 98 <param name="read_group_0|segments|placement" value="fb" /> | |
| 99 <param name="read_group_0|segments|dist_mode" value="ss" /> | |
| 100 <param name="read_group_0|segments|min_size" value="1" /> | |
| 101 <param name="read_group_0|segments|max_size" value="1000" /> | |
| 102 <param name="read_group_0|segments|dist_mode" value="ss" /> | |
| 103 <param name="read_group_0|segments|filename" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> | |
| 104 <param name="min_contig_len" value="200" /> | |
| 105 <output name="out_fasta" file="SRR639755_mito_pairs.clc4_de_novo.fasta" ftype="fasta" /> | |
| 106 </test> | |
| 107 </tests> | |
| 108 <help> | |
| 109 | |
| 110 **What it does** | |
| 111 | |
| 112 Runs the ``clc_assembler`` tool giving a FASTA output file. You would then | |
| 113 typically map the same set of reads onto this assembly using ``cls_mapper`` | |
| 114 to any perform downstream analysis using the mapped reads. | |
| 115 | |
| 116 | |
| 117 **Citation** | |
| 118 | |
| 119 If you use this Galaxy tool in work leading to a scientific publication please | |
| 120 cite this wrapper as: | |
| 121 | |
| 122 Peter J.A. Cock (2013), Galaxy wrapper for the CLC Assembly Cell suite from CLCbio | |
| 123 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell | |
| 124 | |
| 1 | 125 CLC Assembly Cell, CLC bio (2008--2015) |
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46a667b5e19e
v0.0.6 update optional/required parameters and URLS in docs
peterjc
parents:
2
diff
changeset
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126 https://www.qiagenbioinformatics.com/products/clc-assembly-cell/ |
| 1 | 127 |
| 0 | 128 This wrapper is available to install into other Galaxy Instances via the Galaxy |
| 129 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell | |
| 130 </help> | |
| 1 | 131 <citations> |
| 132 <citation type="bibtex"> | |
| 133 @MISC{clcbio, | |
| 134 AUTHOR = {CLC Bio} | |
| 135 title ={{CLC Assembly Cell}}, | |
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46a667b5e19e
v0.0.6 update optional/required parameters and URLS in docs
peterjc
parents:
2
diff
changeset
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136 url = {https://www.qiagenbioinformatics.com/products/clc-assembly-cell/}, |
| 1 | 137 year = {2008--2015} |
| 138 } | |
| 139 </citation> | |
| 140 </citations> | |
| 0 | 141 </tool> |