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comparison crac.xml @ 7:87874e4511be draft default tip

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author bonsai
date Fri, 13 Sep 2013 10:58:42 -0400
parents 9fe9c48f5970
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6:9fe9c48f5970 7:87874e4511be
8 #if $Genome.which_genome == "prebuilt" 8 #if $Genome.which_genome == "prebuilt"
9 <!--1--> "$Genome.prebuilt_genome.fields.path" 9 <!--1--> "$Genome.prebuilt_genome.fields.path"
10 #else 10 #else
11 <!--1--> "$Genome.index_input.extra_files_path" 11 <!--1--> "$Genome.index_input.extra_files_path"
12 #end if 12 #end if
13 #if $condi_compressed == "yes" 13 $compressed
14 --gz
15 #end if
16 <!--2--> $output_name.extra_files_path <!-- Usefull for submitting jobs on crac.sh--> 14 <!--2--> $output_name.extra_files_path <!-- Usefull for submitting jobs on crac.sh-->
17 -r $input -k $kmer_length --read-length $read_length --sam $output_name 15 -r $input -k $kmer_length --read-length $read_length --sam $output_name
18 #if $condi_deep_snp.deepSNP == "yes" 16 #if $condi_deep_snp.deepSNP == "yes"
19 --deep-snv --nb-nucleotides-snv-comparison $condi_deep_snp.nb_nucleotides_snp_comparison 17 --deep-snv --nb-nucleotides-snv-comparison $condi_deep_snp.nb_nucleotides_snp_comparison
20 #end if 18 #end if
28 --max-bases-randomly-matched $choixSettings.max_bases_randomly_matched 26 --max-bases-randomly-matched $choixSettings.max_bases_randomly_matched
29 --max-extension-length $choixSettings.max_extension_length 27 --max-extension-length $choixSettings.max_extension_length
30 --min-support-no-cover $choixSettings.min_support_no_cover 28 --min-support-no-cover $choixSettings.min_support_no_cover
31 --min-break-length $choixSettings.min_break_length 29 --min-break-length $choixSettings.min_break_length
32 #end if 30 #end if
33 #if str($detailed_sam) == "yes" 31 $detailed_sam
34 --detailed-sam
35 #end if
36 32
37 </command> 33 </command>
38 34
39 <inputs> 35 <inputs>
40 <!-- Normal Setting --> 36 <!-- Normal Setting -->
58 <param name="index_input" format="crac_index" type="data" label="Reference Genome" help="Select an indexed Genome from your history"/> 54 <param name="index_input" format="crac_index" type="data" label="Reference Genome" help="Select an indexed Genome from your history"/>
59 </when> 55 </when>
60 </conditional> 56 </conditional>
61 57
62 58
63 <param name="input" format="txt,raw,fastq" type="data" label="Reads File" help="Select a file"/> 59 <param name="input" format="txt,raw,fasta,fastq" type="data" label="Reads file" help="Select a file"/>
64 <param name="kmer_length" type="integer" min="12" max="32" value="22" label="k-mer length"> 60 <param name="kmer_length" type="integer" min="12" max="32" value="22" label="k-mer length">
65 <help>k-mer length must be carefully chosen. A k-mer of that length must map to a unique location in the genome with a high probability. Recommended value for the human genome: 22</help> 61 <help>k-mer length must be carefully chosen. A k-mer of that length must map to a unique location in the genome with a high probability. Recommended value for the human genome: 22</help>
66 </param> 62 </param>
67 <param name="read_length" type="integer" label="Read length" value="0" help="Set read length when all reads have the same length to dramatically increase computation speed. Default value (no read length considered) : 0. Note : If read length is set, shorter reads will be ignored, longer reads will be cut."/> 63 <param name="read_length" type="integer" label="Read length" value="0"
68 <param name="detailed_sam" type="select" label="Do you want a detailed sam output file ?" help="Detailed sam output file gives you information on the SNPs, splice junctions, sequencing errors, chimeras, ..." > 64 help="When all reads have the same length, set the read length to dramatically increase computation speed.
69 <option value="no"> No, I don't want a detailed SAM output file </option> 65 Default value (no read length considered): 0.
70 <option value="yes"> Yes, I want a detailed SAM output file </option> 66 Note : If read length is set, shorter reads will be ignored, longer reads will be cut."/>
71 <when value="yes"/> <!-- Supress warnings--> 67 <param name="detailed_sam" type="select" format="text" label="Do you want a detailed sam output file ?" help="Detailed sam output file gives you information on the SNPs, splice junctions, sequencing errors, chimeras, ..." >
72 <when value="no"/> <!-- Supress warnings--> 68 <option value=""> No, I don't want a detailed SAM output file </option>
69 <option value="--detailed-sam"> Yes, I want a detailed SAM output file </option>
73 </param> 70 </param>
74 <param name="condi_compressed" type="select" display="radio" label="Compress output files?"> 71 <param name="compressed" type="select" display="radio" label="Compress output files?">
75 <option value="yes">Yes</option> 72 <option value="" selected="true">No</option>
76 <option value="no">No</option> 73 <option value="--gz">Yes</option>
77 </param> 74 </param>
78 <conditional name="condi_deep_snp"> <!-- Conditional 1 --> 75 <conditional name="condi_deep_snp"> <!-- Conditional 1 -->
79 <param type="select" name="deepSNP" label="Search hard for SNPs?"> 76 <param type="select" name="deepSNP" label="Search hard for SNPs?">
80 <option value="no" selected="true"> No, do not search hard for SNVs </option> 77 <option value="no" selected="true"> No, do not search hard for SNVs </option>
81 <option value="yes"> Yes, search hard for SNVs (takes more time) </option> 78 <option value="yes"> Yes, search hard for SNVs (takes more time) </option>