Mercurial > repos > devteam > samtools_split
comparison macros.xml @ 4:229681b8c662 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty
author | iuc |
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date | Sun, 28 Jul 2019 14:50:28 -0400 |
parents | ac469d103b51 |
children | 3570a794565c |
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3:ac469d103b51 | 4:229681b8c662 |
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1 <macros> | 1 <macros> |
2 <xml name="requirements"> | 2 <xml name="requirements"> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.3.1">samtools</requirement> | 4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement> |
5 <yield/> | 5 <yield/> |
6 </requirements> | 6 </requirements> |
7 </xml> | 7 </xml> |
8 <token name="@TOOL_VERSION@">1.3.1</token> | 8 <token name="@TOOL_VERSION@">1.9</token> |
9 <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> | |
10 <token name="@PREPARE_IDX@"><![CDATA[ | |
11 ##prepare input and indices | |
12 ln -s '$input' infile && | |
13 #if $input.is_of_type('bam'): | |
14 #if str( $input.metadata.bam_index ) != "None": | |
15 ln -s '${input.metadata.bam_index}' infile.bai && | |
16 #else: | |
17 samtools index infile infile.bai && | |
18 #end if | |
19 #elif $input.is_of_type('cram'): | |
20 #if str( $input.metadata.cram_index ) != "None": | |
21 ln -s '${input.metadata.cram_index}' infile.crai && | |
22 #else: | |
23 samtools index infile infile.crai && | |
24 #end if | |
25 #end if | |
26 ]]></token> | |
27 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ | |
28 ##prepare input and indices | |
29 #for $i, $bam in enumerate( $input_bams ): | |
30 ln -s '$bam' '${i}' && | |
31 #if $bam.is_of_type('bam'): | |
32 #if str( $bam.metadata.bam_index ) != "None": | |
33 ln -s '${bam.metadata.bam_index}' '${i}.bai' && | |
34 #else: | |
35 samtools index '${i}' '${i}.bai' && | |
36 #end if | |
37 #elif $bam.is_of_type('cram'): | |
38 #if str( $bam.metadata.cram_index ) != "None": | |
39 ln -s '${bam.metadata.cram_index}' '${i}.crai' && | |
40 #else: | |
41 samtools index '${i}' '${i}.crai' && | |
42 #end if | |
43 #end if | |
44 #end for | |
45 ]]></token> | |
46 <token name="@PREPARE_FASTA_IDX@"><![CDATA[ | |
47 ##checks for reference data ($addref_cond.addref_select=="history" or =="cached") | |
48 ##and sets the -t/-T parameters accordingly: | |
49 ##- in case of history a symbolic link is used because samtools (view) will generate | |
50 ## the index which might not be possible in the directory containing the fasta file | |
51 ##- in case of cached the absolute path is used which allows to read the cram file | |
52 ## without specifying the reference | |
53 #if $addref_cond.addref_select == "history": | |
54 ln -s '${addref_cond.ref}' reference.fa && | |
55 samtools faidx reference.fa && | |
56 #set reffa="reference.fa" | |
57 #set reffai="reference.fa.fai" | |
58 #elif $addref_cond.addref_select == "cached": | |
59 #set reffa=str($addref_cond.ref.fields.path) | |
60 #set reffai=str($addref_cond.ref.fields.path)+".fai" | |
61 #else | |
62 #set reffa=None | |
63 #set reffai=None | |
64 #end if | |
65 ]]></token> | |
66 <token name="@ADDTHREADS@"><![CDATA[ | |
67 ##compute the number of ADDITIONAL threads to be used by samtools (-@) | |
68 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && | |
69 ]]></token> | |
70 <token name="@ADDMEMORY@"><![CDATA[ | |
71 ##compute the number of memory available to samtools sort (-m) | |
72 ##use only 75% of available: https://github.com/samtools/samtools/issues/831 | |
73 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && | |
74 ((addmemory=addmemory*75/100)) && | |
75 ]]></token> | |
76 <xml name="seed_input"> | |
77 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> | |
78 </xml> | |
79 <xml name="flag_options"> | |
80 <option value="1">read is paired</option> | |
81 <option value="2">read is mapped in a proper pair</option> | |
82 <option value="4">read is unmapped</option> | |
83 <option value="8">mate is unmapped</option> | |
84 <option value="16">read reverse strand</option> | |
85 <option value="32">mate reverse strand</option> | |
86 <option value="64">read is the first in a pair</option> | |
87 <option value="128">read is the second in a pair</option> | |
88 <option value="256">alignment or read is not primary</option> | |
89 <option value="512">read fails platform/vendor quality checks</option> | |
90 <option value="1024">read is a PCR or optical duplicate</option> | |
91 <option value="2048">supplementary alignment</option> | |
92 </xml> | |
93 | |
94 <!-- region specification macros and tokens for tools that allow the specification | |
95 of region by bed file / space separated list of regions --> | |
96 <token name="@REGIONS_FILE@"><![CDATA[ | |
97 #if $cond_region.select_region == 'tab': | |
98 -t '$cond_region.targetregions' | |
99 #end if | |
100 ]]></token> | |
101 <token name="@REGIONS_MANUAL@"><![CDATA[ | |
102 #if $cond_region.select_region == 'text': | |
103 #for $i, $x in enumerate($cond_region.regions_repeat): | |
104 '${x.region}' | |
105 #end for | |
106 #end if | |
107 ]]></token> | |
108 <xml name="regions_macro"> | |
109 <conditional name="cond_region"> | |
110 <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)"> | |
111 <option value="no" selected="True">No</option> | |
112 <option value="text">Manualy specify regions</option> | |
113 <option value="tab">Regions from tabular file</option> | |
114 </param> | |
115 <when value="no"/> | |
116 <when value="text"> | |
117 <repeat name="regions_repeat" min="1" default="1" title="Regions"> | |
118 <param name="region" type="text" label="region" help="format chr:from-to"> | |
119 <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator> | |
120 </param> | |
121 </repeat> | |
122 </when> | |
123 <when value="tab"> | |
124 <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" /> | |
125 </when> | |
126 </conditional> | |
127 </xml> | |
128 | |
9 <xml name="citations"> | 129 <xml name="citations"> |
10 <citations> | 130 <citations> |
11 <citation type="bibtex"> | 131 <citation type="bibtex"> |
12 @misc{SAM_def, | 132 @misc{SAM_def, |
13 title={Definition of SAM/BAM format}, | 133 title={Definition of SAM/BAM format}, |
47 <xml name="stdio"> | 167 <xml name="stdio"> |
48 <stdio> | 168 <stdio> |
49 <exit_code range="1:" level="fatal" description="Error" /> | 169 <exit_code range="1:" level="fatal" description="Error" /> |
50 </stdio> | 170 </stdio> |
51 </xml> | 171 </xml> |
52 <token name="@no-chrom-options@"> | |
53 ----- | |
54 | |
55 .. class:: warningmark | |
56 | |
57 **No options available? How to re-detect metadata** | |
58 | |
59 If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: | |
60 | |
61 1. Click on the **pencil** icon adjacent to the dataset in the history | |
62 2. A new menu will appear in the center pane of the interface | |
63 3. Click **Datatype** tab | |
64 4. Set **New Type** to **BAM** | |
65 5. Click **Save** | |
66 | |
67 The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. | |
68 </token> | |
69 </macros> | 172 </macros> |