Mercurial > repos > devteam > sam_to_bam

annotate sam_to_bam.xml @ 13:0e60e2dd20af 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/master/tool_collections/samtools/sam_to_bam commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:25:11 +0000
parents 9bd1568619cd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
1 <tool id="sam_to_bam" name="SAM-to-BAM" version="2.1.2" profile="@PROFILE@">
8
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
2 <description>convert SAM to BAM</description>
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
3
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
4 <macros>
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
5 <import>macros.xml</import>
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
6 </macros>
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
7 <expand macro="requirements"/>
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
8 <expand macro="stdio"/>
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
9 <expand macro="version_command"/>
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
10
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
11 <command><![CDATA[
11
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
12 @ADDTHREADS@
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
13 @ADDMEMORY@
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
14 @PREPARE_FASTA_IDX@
8
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
15
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
16 samtools view
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
17 -b
11
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
18 -@ \$addthreads
12
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
19 -t "\$reffai"
11
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
20 '$input' |
8
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
21
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
22 samtools sort
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
23 -O bam
11
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
24 -@ \$addthreads -m \$addmemory"M"
8
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
25 -o '$output1'
10
cf1ffd88f895 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents: 8
diff changeset
26 -T "\${TMPDIR:-.}"
8
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
27 ]]></command>
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
28
6
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
29 <inputs>
11
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
30 <param name="input" type="data" format="sam" label="SAM file to convert"/>
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
31 <expand macro="mandatory_reference" argument="-t"/>
6
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
32 </inputs>
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
33 <outputs>
8
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
34 <data name="output1" format="bam" label="${tool.name} on ${on_string}: converted BAM">
6
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
35 <actions>
11
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
36 <conditional name="addref_cond.addref_select">
6
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
37 <when value="cached">
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
38 <action name="dbkey" type="metadata">
11
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
39 <option name="input" param_attribute="dbkey" type="from_param" />
6
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
40 </action>
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
41 </when>
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
42 <when value="history">
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
43 <action name="dbkey" type="metadata">
11
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
44 <option name="addref_cond.ref" param_attribute="dbkey" type="from_param" />
6
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
45 </action>
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
46 </when>
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
47 </conditional>
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
48 </actions>
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
49 </data>
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
50 </outputs>
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
51 <tests>
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
52 <test>
11
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
53 <param name="addref_select" value="history" />
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
54 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
55 <param name="input" ftype="sam" value="sam_to_bam_in1.sam" />
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
56 <output name="output1" ftype="bam" file="sam_to_bam_out1.bam" lines_diff="4"/>
8
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
57 </test>
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
58 <test>
11
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
59 <param name="addref_select" value="cached" />
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
60 <param name="ref" value="equCab2chrM" />
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
61 <param name="input" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" />
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
62 <output name="output1" ftype="bam" file="sam_to_bam_out2.bam" lines_diff="4"/>
6
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
63 </test>
7
881e16ad05c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/sam_to_bam commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
64 <test>
11
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
65 <param name="addref_select" value="history" />
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
66 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
67 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
1e69848b596f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 10
diff changeset
68 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
7
881e16ad05c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/sam_to_bam commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
69 </test>
12
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
70 <test>
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
71 <!-- Test direct use of bgzipped reference -->
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
72 <param name="addref_select" value="history" />
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
73 <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.bgzipped_fasta.gz" />
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
74 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
75 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
76 </test>
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
77 <test>
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
78 <!-- Test with simple gzipped reference, which requires decompression -->
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
79 <param name="addref_select" value="history" />
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
80 <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.fasta.gz" />
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
81 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
82 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
9bd1568619cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 11
diff changeset
83 </test>
6
d04d9f1c6791 Uploaded
devteam
parents: 5
diff changeset
84 </tests>
8
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
85 <help><![CDATA[
0
30fdbaccb96b Uploaded tool tarball.
devteam
parents:
diff changeset
86 **What it does**
30fdbaccb96b Uploaded tool tarball.
devteam
parents:
diff changeset
87
8
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
88 Converts SAM dataset into its binary, BAM, representation using the ``samtools view`` and ``sort`` commands.
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
89 ]]></help>
f7a0d41036c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 7
diff changeset
90 <expand macro="citations"/>
0
30fdbaccb96b Uploaded tool tarball.
devteam
parents:
diff changeset
91 </tool>