Mercurial > repos > devteam > samtools_slice_bam
comparison macros.xml @ 4:344fc91e1bfd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author | iuc |
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date | Tue, 28 Sep 2021 16:16:30 +0000 |
parents | a4a10c7924d1 |
children | b5c88b7b153e |
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3:a4a10c7924d1 | 4:344fc91e1bfd |
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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@">1.13</token> |
9 <token name="@PROFILE@">20.05</token> | |
10 <token name="@FLAGS@"><![CDATA[ | |
11 #set $flags = 0 | |
12 #if $filter | |
13 #set $flags = sum(map(int, str($filter).split(','))) | |
14 #end if | |
15 ]]></token> | |
16 <token name="@PREPARE_IDX@"><![CDATA[ | |
17 ##prepare input and indices | |
18 ln -s '$input' infile && | |
19 #if $input.is_of_type('bam'): | |
20 #if str( $input.metadata.bam_index ) != "None": | |
21 ln -s '${input.metadata.bam_index}' infile.bai && | |
22 #else: | |
23 samtools index infile infile.bai && | |
24 #end if | |
25 #elif $input.is_of_type('cram'): | |
26 #if str( $input.metadata.cram_index ) != "None": | |
27 ln -s '${input.metadata.cram_index}' infile.crai && | |
28 #else: | |
29 samtools index infile infile.crai && | |
30 #end if | |
31 #end if | |
32 ]]></token> | |
33 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ | |
34 ##prepare input and indices | |
35 #for $i, $bam in enumerate( $input_bams ): | |
36 ln -s '$bam' '${i}' && | |
37 #if $bam.is_of_type('bam'): | |
38 #if str( $bam.metadata.bam_index ) != "None": | |
39 ln -s '${bam.metadata.bam_index}' '${i}.bai' && | |
40 #else: | |
41 samtools index '${i}' '${i}.bai' && | |
42 #end if | |
43 #elif $bam.is_of_type('cram'): | |
44 #if str( $bam.metadata.cram_index ) != "None": | |
45 ln -s '${bam.metadata.cram_index}' '${i}.crai' && | |
46 #else: | |
47 samtools index '${i}' '${i}.crai' && | |
48 #end if | |
49 #end if | |
50 #end for | |
51 ]]></token> | |
52 <token name="@PREPARE_FASTA_IDX@"><![CDATA[ | |
53 ##checks for reference data ($addref_cond.addref_select=="history" or =="cached") | |
54 ##and sets the -t/-T parameters accordingly: | |
55 ##- in case of history a symbolic link is used because samtools (view) will generate | |
56 ## the index which might not be possible in the directory containing the fasta file | |
57 ##- in case of cached the absolute path is used which allows to read the cram file | |
58 ## without specifying the reference | |
59 #if $addref_cond.addref_select == "history": | |
60 ln -s '${addref_cond.ref}' reference.fa && | |
61 samtools faidx reference.fa && | |
62 #set reffa="reference.fa" | |
63 #set reffai="reference.fa.fai" | |
64 #elif $addref_cond.addref_select == "cached": | |
65 #set reffa=str($addref_cond.ref.fields.path) | |
66 #set reffai=str($addref_cond.ref.fields.path)+".fai" | |
67 #else | |
68 #set reffa=None | |
69 #set reffai=None | |
70 #end if | |
71 ]]></token> | |
72 | |
73 <xml name="optional_reference"> | |
74 <conditional name="addref_cond"> | |
75 <param name="addref_select" type="select" label="Use a reference sequence"> | |
76 <help>@HELP@</help> | |
77 <option value="no">No</option> | |
78 <option value="history">Use a genome/index from the history</option> | |
79 <option value="cached">Use a built-in genome</option> | |
80 </param> | |
81 <when value="no"/> | |
82 <when value="history"> | |
83 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> | |
84 </when> | |
85 <when value="cached"> | |
86 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> | |
87 <options from_data_table="fasta_indexes"> | |
88 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> | |
89 </options> | |
90 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/> | |
91 </param> | |
92 </when> | |
93 </conditional> | |
94 </xml> | |
95 <xml name="mandatory_reference" token_help="" token_argument=""> | |
96 <conditional name="addref_cond"> | |
97 <param name="addref_select" type="select" label="Use a reference sequence"> | |
98 <help>@HELP@</help> | |
99 <option value="history">Use a genome/index from the history</option> | |
100 <option value="cached">Use a built-in genome</option> | |
101 </param> | |
102 <when value="history"> | |
103 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> | |
104 </when> | |
105 <when value="cached"> | |
106 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> | |
107 <options from_data_table="fasta_indexes"> | |
108 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> | |
109 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> | |
110 </options> | |
111 </param> | |
112 </when> | |
113 </conditional> | |
114 </xml> | |
115 | |
116 | |
117 <token name="@ADDTHREADS@"><![CDATA[ | |
118 ##compute the number of ADDITIONAL threads to be used by samtools (-@) | |
119 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && | |
120 ]]></token> | |
121 <token name="@ADDMEMORY@"><![CDATA[ | |
122 ##compute the number of memory available to samtools sort (-m) | |
123 ##use only 75% of available: https://github.com/samtools/samtools/issues/831 | |
124 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && | |
125 ((addmemory=addmemory*75/100)) && | |
126 ]]></token> | |
127 <xml name="seed_input"> | |
128 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> | |
129 </xml> | |
130 <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false"> | |
131 <option value="1" selected="@S1@">Read is paired</option> | |
132 <option value="2" selected="@S2@">Read is mapped in a proper pair</option> | |
133 <option value="4" selected="@S4@">Read is unmapped</option> | |
134 <option value="8" selected="@S8@">Mate is unmapped</option> | |
135 <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option> | |
136 <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option> | |
137 <option value="64" selected="@S64@">Read is the first in a pair</option> | |
138 <option value="128" selected="@S128@">Read is the second in a pair</option> | |
139 <option value="256" selected="@S256@">Alignment of the read is not primary</option> | |
140 <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option> | |
141 <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option> | |
142 <option value="2048" selected="@S2048@">Alignment is supplementary</option> | |
143 </xml> | |
144 | |
145 <!-- region specification macros and tokens for tools that allow the specification | |
146 of region by bed file / space separated list of regions --> | |
147 <token name="@REGIONS_FILE@"><![CDATA[ | |
148 #if $cond_region.select_region == 'tab': | |
149 -t '$cond_region.targetregions' | |
150 #end if | |
151 ]]></token> | |
152 <token name="@REGIONS_MANUAL@"><![CDATA[ | |
153 #if $cond_region.select_region == 'text': | |
154 #for $i, $x in enumerate($cond_region.regions_repeat): | |
155 '${x.region}' | |
156 #end for | |
157 #end if | |
158 ]]></token> | |
159 <xml name="regions_macro"> | |
160 <conditional name="cond_region"> | |
161 <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)"> | |
162 <option value="no" selected="True">No</option> | |
163 <option value="text">Manualy specify regions</option> | |
164 <option value="tab">Regions from tabular file</option> | |
165 </param> | |
166 <when value="no"/> | |
167 <when value="text"> | |
168 <repeat name="regions_repeat" min="1" default="1" title="Regions"> | |
169 <param name="region" type="text" label="region" help="format chr:from-to"> | |
170 <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator> | |
171 </param> | |
172 </repeat> | |
173 </when> | |
174 <when value="tab"> | |
175 <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)" /> | |
176 </when> | |
177 </conditional> | |
178 </xml> | |
179 | |
9 <xml name="citations"> | 180 <xml name="citations"> |
10 <citations> | 181 <citations> |
11 <citation type="bibtex"> | 182 <citation type="bibtex"> |
12 @misc{SAM_def, | 183 @misc{SAM_def, |
13 title={Definition of SAM/BAM format}, | 184 title={Definition of SAM/BAM format}, |
47 <xml name="stdio"> | 218 <xml name="stdio"> |
48 <stdio> | 219 <stdio> |
49 <exit_code range="1:" level="fatal" description="Error" /> | 220 <exit_code range="1:" level="fatal" description="Error" /> |
50 </stdio> | 221 </stdio> |
51 </xml> | 222 </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> | 223 </macros> |