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1 <tool id="igvtools_sort" name="IGVtools sort" version="1.0">
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2 <description>input file by start position</description>
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3 <command interpreter="bash">igvtools sort -t .
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4 ## IGVTools relies on the file extension to determine format
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5 #if $input.datatype.file_ext == 'vcf':
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6 #set $input_name='input_file.vcf'
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7 #set $output_name='output.vcf'
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8 #elif $input.datatype.file_ext == 'sam':
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9 #set $input_name='input_file.sam'
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10 #set $output_name='output.sam'
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11 #elif $input.datatype.file_ext == 'bed':
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12 #set $input_name='input_file.bed'
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13 #set $output_name='output.bed'
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14 #elif $input.datatype.file_ext == 'psl':
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15 #set $input_name='input_file.psl'
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16 #set $output_name='output.psl'
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17 #elif $input.datatype.file_ext == 'igv':
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18 #set $input_name='input_file.igv'
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19 #set $output_name='output.igv'
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20 #elif $input.datatype.file_ext == 'igv.cn':
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21 #set $input_name='input_file.cn'
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22 #set $output_name='output.cn'
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23 #end if
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24 `ln -s $input $input_name; echo $input_name` $output_name
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25 </command>
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26 <inputs>
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27 <param name="input" type="data" format="sam,bed,vcf,psl,igv,igv.cn," label="Input file SAM,BED,VCF format"
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28 help="Use samtools or picard to sort bam files"/>
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29 </inputs>
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30 <outputs>
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31 <data format_source="input" name="output_sam" metadata_source="input" label="${tool.name} on ${on_string}: igv.sam" from_work_dir="output.sam">
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32 <filter>(input.datatype.file_ext == 'sam')</filter>
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33 </data>
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34 <data format_source="input" name="output_bed" metadata_source="input" label="${tool.name} on ${on_string}: igv.bed" from_work_dir="output.bed">
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35 <filter>(input.datatype.file_ext == 'bed')</filter>
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36 </data>
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37 <data format_source="input" name="output_vcf" metadata_source="input" label="${tool.name} on ${on_string}: igv.vcf" from_work_dir="output.vcf">
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38 <filter>(input.datatype.file_ext == 'vcf')</filter>
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39 </data>
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40 <data format_source="input" name="output_psl" metadata_source="input" label="${tool.name} on ${on_string}: igv.vcf" from_work_dir="output.psl">
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41 <filter>(input.datatype.file_ext == 'psl')</filter>
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42 </data>
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43 <data format_source="input" name="output_igv" metadata_source="input" label="${tool.name} on ${on_string}: igv" from_work_dir="output.igv">
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44 <filter>(input.datatype.file_ext == 'igv')</filter>
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45 </data>
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46 <data format_source="input" name="output_cn" metadata_source="input" label="${tool.name} on ${on_string}: igv.cn" from_work_dir="output.cn">
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47 <filter>(input.datatype.file_ext == 'igv.cn')</filter>
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48 </data>
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49 </outputs>
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50 <tests>
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51 </tests>
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52 <help>
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53 **What it does**
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54
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55 The IGVTools_ sort command sorts the input file by start position, as required.
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56
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57 .. _IGVTools: http://www.broadinstitute.org/software/igv/igvtools_commandline
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58 .. _IGV: http://www.broadinstitute.org/igv/
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59
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60 ------
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61
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62 To cite your use of IGV in your publication::
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63
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64 James T. Robinson, Helga Thorvaldsdottir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov.
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65 Integrative Genomics Viewer. Nature Biotechnology 29, 24-26 (2011)
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66
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67 ------
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68
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69 **Input formats**
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70
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71 Supported input file formats are: .cn, .igv, .sam, .aligned, .psl, .bed, and .vcf.
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72
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73 ------
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74
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75 **Outputs**
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76
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77 The output will have the same format as the input file.
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78
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79 </help>
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80 </tool>
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