Mercurial > repos > devteam > sam_pileup
comparison sam_pileup.xml @ 1:e7d863c5c5d6
Update sam_pileup to use the fasta_indexes data table.
author | Dave Bouvier <dave@bx.psu.edu> |
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date | Wed, 11 Dec 2013 12:54:32 -0500 |
parents | 95612c159681 |
children | 3ff8935743a9 |
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0:95612c159681 | 1:e7d863c5c5d6 |
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1 <tool id="sam_pileup" name="Generate pileup" version="1.1.1"> | 1 <tool id="sam_pileup" name="Generate pileup" version="1.1.2"> |
2 <description>from BAM dataset</description> | 2 <description>from BAM dataset</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.1.16">samtools</requirement> | 4 <requirement type="package" version="0.1.16">samtools</requirement> |
5 </requirements> | 5 </requirements> |
6 <command interpreter="python"> | 6 <command interpreter="python"> |
9 --output=$output1 | 9 --output=$output1 |
10 --ref=$refOrHistory.reference | 10 --ref=$refOrHistory.reference |
11 #if $refOrHistory.reference == "history": | 11 #if $refOrHistory.reference == "history": |
12 --ownFile=$refOrHistory.ownFile | 12 --ownFile=$refOrHistory.ownFile |
13 #else: | 13 #else: |
14 --ownFile="None" | 14 --index=${refOrHistory.index.fields.path} |
15 #end if | 15 #end if |
16 --dbkey=${input1.metadata.dbkey} | 16 --dbkey=${input1.metadata.dbkey} |
17 --indexDir=${GALAXY_DATA_INDEX_DIR} | 17 --indexDir=${GALAXY_DATA_INDEX_DIR} |
18 --bamIndex=${input1.metadata.bam_index} | 18 --bamIndex=${input1.metadata.bam_index} |
19 --lastCol=$lastCol | 19 --lastCol=$lastCol |
39 <option value="history">Use one from the history</option> | 39 <option value="history">Use one from the history</option> |
40 </param> | 40 </param> |
41 <when value="indexed"> | 41 <when value="indexed"> |
42 <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for"> | 42 <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for"> |
43 <validator type="unspecified_build" /> | 43 <validator type="unspecified_build" /> |
44 <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" /> | 44 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> |
45 | |
46 </param> | |
47 <param name="index" type="select" label="Using reference genome"> | |
48 <options from_data_table="fasta_indexes"> | |
49 <filter type="data_meta" ref="input1" key="dbkey" column="1" /> | |
50 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> | |
51 </options> | |
45 </param> | 52 </param> |
46 </when> | 53 </when> |
47 <when value="history"> | 54 <when value="history"> |
48 <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for" /> | 55 <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for" /> |
49 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" /> | 56 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" /> |
98 samtools pileup -M 60 -c -T 0.85 -N 2 -r 0.001 -I 40 -f chr_m.fasta test-data/sam_pileup_in1.bam > sam_pileup_out2.pileup | 105 samtools pileup -M 60 -c -T 0.85 -N 2 -r 0.001 -I 40 -f chr_m.fasta test-data/sam_pileup_in1.bam > sam_pileup_out2.pileup |
99 chr_m.fasta is the prefix of the index | 106 chr_m.fasta is the prefix of the index |
100 --> | 107 --> |
101 <param name="reference" value="indexed" /> | 108 <param name="reference" value="indexed" /> |
102 <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" /> | 109 <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" /> |
110 <param name="index" value="chr_m" /> | |
103 <param name="lastCol" value="no" /> | 111 <param name="lastCol" value="no" /> |
104 <param name="indels" value="no" /> | 112 <param name="indels" value="no" /> |
105 <param name="mapCap" value="60" /> | 113 <param name="mapCap" value="60" /> |
106 <param name="consensus" value="yes" /> | 114 <param name="consensus" value="yes" /> |
107 <param name="theta" value="0.85" /> | 115 <param name="theta" value="0.85" /> |