Mercurial > repos > iuc > samtools_faidx

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
1 <tool id="samtools_faidx" name="Samtools faidx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
2 <description>Index a FASTA file</description>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
3 <macros>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
4 <import>macros.xml</import>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
5 </macros>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
7 <expand macro="stdio"/>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
8 <expand macro="version_command"/>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
9 <command><![CDATA[
1
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
10 #set is_fastq = ("fastq" in $input.ext)
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
11 #if $input.ext.endswith(".gz") or $input.ext.endswith(".bgz") or $input.ext == "bgzip"
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
12 ln -s '$input' input.gz &&
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
13 samtools faidx
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
14 #if $is_fastq
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
15 --fastq
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
16 #end if
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
17 input.gz
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
18 --fai-idx '$output'
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
19 --gzi-idx input.gz.gzi
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
20 || (
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
21 echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 &&
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
22 gzip -dc input.gz > input.plain &&
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
23 samtools faidx
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
24 #if $is_fastq
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
25 --fastq
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
26 #end if
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
27 input.plain
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
28 --fai-idx '$output'
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
29 )
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
30 #else
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
31 ln -s '$input' input &&
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
32 samtools faidx
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
33 #if $is_fastq
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
34 --fastq
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
35 #end if
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
36 input
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
37 --fai-idx '$output'
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
38 #end if
0
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
39 ]]></command>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
40 <inputs>
1
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
41 <param name="input"
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
42 type="data"
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
43 format="fasta,fasta.gz,fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz"
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
44 label="Dataset with sequences (FASTA or FASTQ; auto-detected)" />
0
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
45 </inputs>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
46 <outputs>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
47 <data name="output" format="tabular"/>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
48 </outputs>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
49 <tests>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
50 <test expect_num_outputs="1">
1
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
51 <param name="input" value="samtools_fastx-out1-2.fasta" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
52 <output name="output" file="out_fasta.tabular" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
53 </test>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
54 <test expect_num_outputs="1">
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
55 <param name="input" value="samtools_fastx-out1-2.fasta.gz" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
56 <output name="output" file="out_fasta.tabular" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
57 <assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
58 <has_line line="Failed to index compressed reference. Trying decompressed ..." />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
59 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip"/>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
60 </assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
61 </test>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
62 <test expect_num_outputs="1">
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
63 <param name="input" value="samtools_fastx-out1-2.fasta.bgz" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
64 <output name="output" file="out_fasta.tabular" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
65 <assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
66 <has_line line="Failed to index compressed reference. Trying decompressed ..." negate="true" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
67 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip" negate="true"/>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
68 </assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
69 </test>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
70 <test expect_num_outputs="1">
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
71 <param name="input" value="samtools_fastx-out1-2.fastq" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
72 <output name="output" file="out_fastq.tabular" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
73 </test>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
74 <test expect_num_outputs="1">
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
75 <param name="input" value="samtools_fastx-out1-2.fastq.gz" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
76 <output name="output" file="out_fastq.tabular" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
77 <assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
78 <has_line line="Failed to index compressed reference. Trying decompressed ..."/>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
79 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip"/>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
80 </assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
81 </test>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
82 <test expect_num_outputs="1">
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
83 <param name="input" value="samtools_fastx-out1-2.fastq.bgz" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
84 <output name="output" file="out_fastq.tabular" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
85 <assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
86 <has_line line="Failed to index compressed reference. Trying decompressed ..." negate="true"/>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
87 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip" negate="true"/>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
88 </assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
89 </test>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
90 <test expect_num_outputs="1">
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
91 <param name="input" value="samtools_fastx-out1-2.fastq" ftype="fastqsanger" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
92 <output name="output" file="out_fastq.tabular" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
93 </test>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
94 <test expect_num_outputs="1">
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
95 <param name="input" value="samtools_fastx-out1-2.fastq.gz" ftype="fastqsanger.gz" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
96 <output name="output" file="out_fastq.tabular" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
97 <assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
98 <has_line line="Failed to index compressed reference. Trying decompressed ..." />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
99 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
100 </assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
101 </test>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
102 <test expect_num_outputs="1">
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
103 <param name="input" value="samtools_fastx-out1-2.fastq.bgz" ftype="fastqsanger.gz" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
104 <output name="output" file="out_fastq.tabular" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
105 <assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
106 <has_line line="Failed to index compressed reference. Trying decompressed ..." negate="true" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
107 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip" negate="true" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
108 </assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
109 </test>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
110 <test expect_num_outputs="1">
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
111 <param name="input" value="samtools_fastx-out1-2.fastq" ftype="fastqillumina" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
112 <output name="output" file="out_fastq.tabular" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
113 </test>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
114 <test expect_num_outputs="1">
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
115 <param name="input" value="samtools_fastx-out1-2.fastq.gz" ftype="fastqillumina.gz" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
116 <output name="output" file="out_fastq.tabular" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
117 <assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
118 <has_line line="Failed to index compressed reference. Trying decompressed ..." />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
119 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
120 </assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
121 </test>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
122 <test>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
123 <param name="input" value="samtools_fastx-out1-2.fastq.bgz" ftype="fastqillumina.gz" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
124 <output name="output" file="out_fastq.tabular" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
125 <assert_stderr>
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
126 <has_line line="Failed to index compressed reference. Trying decompressed ..." negate="true" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
127 <has_line line="[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip" negate="true" />
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
128 </assert_stderr>
0
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
129 </test>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
130 </tests>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
131 <help><![CDATA[
1
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
132 **What it does**
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
133
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
134 Runs the ``samtools faidx`` command to index reference sequence in the FASTA format reference sequence.
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
135
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
136 If the input file is of ``fastq`` type, passes the --fastq flag to accomodate the ``samtools faidx`` command line tool.
0
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
137
1
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
138 **Notes on compression**
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
139 - ``samtools faidx`` supports **BGZF-compressed** FASTA files (e.g. ``.fa.bgz`` / ``.fasta.bgz``).
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
140 - Plain ``.fasta.gz`` may need to be decompressed first, depending on how it was created.
0
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
141
1
76c27c4861bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit 7ba11a2aa8901b555a95e284e4fb83c8dca2833e
iuc
parents: 0
diff changeset
142 Full `documentation <https://www.htslib.org/doc/samtools-faidx.html>`_ for the faidx command.
0
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
143 ]]></help>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
144 <expand macro="citations"/>
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
145 </tool>