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comparison samtools_faidx.xml @ 1:76c27c4861bd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
author iuc
date Tue, 04 Nov 2025 22:34:23 +0000
parents baa79754a17e
children
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0:baa79754a17e 1:76c27c4861bd
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 samtools 10 #set is_fastq = ("fastq" in $input.ext)
11 faidx 11 #if $input.ext.endswith(".gz") or $input.ext.endswith(".bgz") or $input.ext == "bgzip"
12 '$in_fasta' 12 ln -s '$input' input.gz &&
13 --fai-idx '$output' 13 samtools faidx
14 #if $is_fastq
15 --fastq
16 #end if
17 input.gz
18 --fai-idx '$output'
19 --gzi-idx input.gz.gzi
20 || (
21 echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 &&
22 gzip -dc input.gz > input.plain &&
23 samtools faidx
24 #if $is_fastq
25 --fastq
26 #end if
27 input.plain
28 --fai-idx '$output'
29 )
30 #else
31 ln -s '$input' input &&
32 samtools faidx
33 #if $is_fastq
34 --fastq
35 #end if
36 input
37 --fai-idx '$output'
38 #end if
14 ]]></command> 39 ]]></command>
15 <inputs> 40 <inputs>
16 <param name="in_fasta" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="dataset with sequences" /> 41 <param name="input"
42 type="data"
43 format="fasta,fasta.gz,fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz"
44 label="Dataset with sequences (FASTA or FASTQ; auto-detected)" />
17 </inputs> 45 </inputs>
18 <outputs> 46 <outputs>
19 <data name="output" format="tabular"/> 47 <data name="output" format="tabular"/>
20 </outputs> 48 </outputs>
21 <tests> 49 <tests>
22 <test expect_num_outputs="1"> 50 <test expect_num_outputs="1">
23 <param name="in_fasta" value="samtools_fastx-out1-2.fasta" /> 51 <param name="input" value="samtools_fastx-out1-2.fasta" />
24 <output name="output" file="out.tabular" /> 52 <output name="output" file="out_fasta.tabular" />
53 </test>
54 <test expect_num_outputs="1">
55 <param name="input" value="samtools_fastx-out1-2.fasta.gz" />
56 <output name="output" file="out_fasta.tabular" />
57 <assert_stderr>
58 <has_line line="Failed to index compressed reference. Trying decompressed ..." />
59 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip"/>
60 </assert_stderr>
61 </test>
62 <test expect_num_outputs="1">
63 <param name="input" value="samtools_fastx-out1-2.fasta.bgz" />
64 <output name="output" file="out_fasta.tabular" />
65 <assert_stderr>
66 <has_line line="Failed to index compressed reference. Trying decompressed ..." negate="true" />
67 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip" negate="true"/>
68 </assert_stderr>
69 </test>
70 <test expect_num_outputs="1">
71 <param name="input" value="samtools_fastx-out1-2.fastq" />
72 <output name="output" file="out_fastq.tabular" />
73 </test>
74 <test expect_num_outputs="1">
75 <param name="input" value="samtools_fastx-out1-2.fastq.gz" />
76 <output name="output" file="out_fastq.tabular" />
77 <assert_stderr>
78 <has_line line="Failed to index compressed reference. Trying decompressed ..."/>
79 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip"/>
80 </assert_stderr>
81 </test>
82 <test expect_num_outputs="1">
83 <param name="input" value="samtools_fastx-out1-2.fastq.bgz" />
84 <output name="output" file="out_fastq.tabular" />
85 <assert_stderr>
86 <has_line line="Failed to index compressed reference. Trying decompressed ..." negate="true"/>
87 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip" negate="true"/>
88 </assert_stderr>
89 </test>
90 <test expect_num_outputs="1">
91 <param name="input" value="samtools_fastx-out1-2.fastq" ftype="fastqsanger" />
92 <output name="output" file="out_fastq.tabular" />
93 </test>
94 <test expect_num_outputs="1">
95 <param name="input" value="samtools_fastx-out1-2.fastq.gz" ftype="fastqsanger.gz" />
96 <output name="output" file="out_fastq.tabular" />
97 <assert_stderr>
98 <has_line line="Failed to index compressed reference. Trying decompressed ..." />
99 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip" />
100 </assert_stderr>
101 </test>
102 <test expect_num_outputs="1">
103 <param name="input" value="samtools_fastx-out1-2.fastq.bgz" ftype="fastqsanger.gz" />
104 <output name="output" file="out_fastq.tabular" />
105 <assert_stderr>
106 <has_line line="Failed to index compressed reference. Trying decompressed ..." negate="true" />
107 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip" negate="true" />
108 </assert_stderr>
109 </test>
110 <test expect_num_outputs="1">
111 <param name="input" value="samtools_fastx-out1-2.fastq" ftype="fastqillumina" />
112 <output name="output" file="out_fastq.tabular" />
113 </test>
114 <test expect_num_outputs="1">
115 <param name="input" value="samtools_fastx-out1-2.fastq.gz" ftype="fastqillumina.gz" />
116 <output name="output" file="out_fastq.tabular" />
117 <assert_stderr>
118 <has_line line="Failed to index compressed reference. Trying decompressed ..." />
119 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip" />
120 </assert_stderr>
121 </test>
122 <test>
123 <param name="input" value="samtools_fastx-out1-2.fastq.bgz" ftype="fastqillumina.gz" />
124 <output name="output" file="out_fastq.tabular" />
125 <assert_stderr>
126 <has_line line="Failed to index compressed reference. Trying decompressed ..." negate="true" />
127 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip" negate="true" />
128 </assert_stderr>
25 </test> 129 </test>
26 </tests> 130 </tests>
27 <help><![CDATA[ 131 <help><![CDATA[
28 **What it does** 132 **What it does**
29 133
30 Runs the ``samtools faidx`` command to index reference sequence in the FASTA format reference sequence. 134 Runs the ``samtools faidx`` command to index reference sequence in the FASTA format reference sequence.
31 135
32 Full `documentation <https://www.htslib.org/doc/samtools-faidx.html>`_ for the faidx command. 136 If the input file is of ``fastq`` type, passes the --fastq flag to accomodate the ``samtools faidx`` command line tool.
137
138 **Notes on compression**
139 - ``samtools faidx`` supports **BGZF-compressed** FASTA files (e.g. ``.fa.bgz`` / ``.fasta.bgz``).
140 - Plain ``.fasta.gz`` may need to be decompressed first, depending on how it was created.
141
142 Full `documentation <https://www.htslib.org/doc/samtools-faidx.html>`_ for the faidx command.
33 ]]></help> 143 ]]></help>
34 <expand macro="citations"/> 144 <expand macro="citations"/>
35 </tool> 145 </tool>