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comparison sam_pileup.xml @ 1:efd77ef84903 draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:30:34 -0400
parents cb3966035753
children 37df866ccf1a
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0:cb3966035753 1:efd77ef84903
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=${input1.metadata.dbkey}
17 --indexDir=${GALAXY_DATA_INDEX_DIR}
18 --bamIndex=${input1.metadata.bam_index} 16 --bamIndex=${input1.metadata.bam_index}
19 --lastCol=$lastCol 17 --lastCol=$lastCol
20 --indels=$indels 18 --indels=$indels
21 --mapCap=$mapCap 19 --mapCap=$mapCap
22 --consensus=$c.consensus 20 --consensus=$c.consensus
39 <option value="history">Use one from the history</option> 37 <option value="history">Use one from the history</option>
40 </param> 38 </param>
41 <when value="indexed"> 39 <when value="indexed">
42 <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for"> 40 <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for">
43 <validator type="unspecified_build" /> 41 <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" /> 42 <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." />
43
44 </param>
45 <param name="index" type="select" label="Using reference genome">
46 <options from_data_table="fasta_indexes">
47 <filter type="data_meta" ref="input1" key="dbkey" column="1" />
48 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
49 </options>
45 </param> 50 </param>
46 </when> 51 </when>
47 <when value="history"> 52 <when value="history">
48 <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for" /> 53 <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" /> 54 <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 103 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 104 chr_m.fasta is the prefix of the index
100 --> 105 -->
101 <param name="reference" value="indexed" /> 106 <param name="reference" value="indexed" />
102 <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" /> 107 <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" />
108 <param name="index" value="chr_m" />
103 <param name="lastCol" value="no" /> 109 <param name="lastCol" value="no" />
104 <param name="indels" value="no" /> 110 <param name="indels" value="no" />
105 <param name="mapCap" value="60" /> 111 <param name="mapCap" value="60" />
106 <param name="consensus" value="yes" /> 112 <param name="consensus" value="yes" />
107 <param name="theta" value="0.85" /> 113 <param name="theta" value="0.85" />