Mercurial > repos > iuc > samtools_faidx

annotate samtools_faidx.xml @ 0:baa79754a17e draft

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 da2aa10802e960a69f3858f86b858807442ca7c7
author iuc
date Mon, 12 May 2025 18:06:17 +0000
parents
children 76c27c4861bd
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[
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
10 samtools
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
11 faidx
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
12 '$in_fasta'
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
13 --fai-idx '$output'
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
14 ]]></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
15 <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
16 <param name="in_fasta" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="dataset with sequences" />
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
17 </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
18 <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
19 <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
20 </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
21 <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
22 <test expect_num_outputs="1">
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
23 <param name="in_fasta" value="samtools_fastx-out1-2.fasta" />
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
24 <output name="output" file="out.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
25 </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
26 </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
27 <help><![CDATA[
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
28 **What it does**
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
29
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
30 Runs the ``samtools faidx`` command to index reference sequence in the FASTA format reference sequence.
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
31
baa79754a17e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
iuc
parents:
diff changeset
32 Full `documentation <https://www.htslib.org/doc/samtools-faidx.html>`_ for the faidx 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
33 ]]></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
34 <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
35 </tool>