annotate samtools_cram_to_bam.xml @ 7:974fe4f4e52b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit cd62639660bef041ba14ecff337fb98e84e75d8a
author iuc
date Mon, 20 Nov 2023 22:14:11 +0000
parents 55ae400c0cc4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
974fe4f4e52b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 6
diff changeset
1 <tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
2 <description>convert CRAM alignments to BAM format</description>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
3
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
4 <macros>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
5 <import>macros.xml</import>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
6 </macros>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
8 <expand macro="stdio"/>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
9 <expand macro="version_command"/>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
10
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
11 <command><![CDATA[
4
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
12 @ADDTHREADS@
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
13 ln -s '$input' input.cram &&
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
14 #if str( $input.metadata.cram_index ) != "None":
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
15 ln -f -s '${input.metadata.cram_index}' input.cram.crai &&
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
16 #end if
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
17
4
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
18 @PREPARE_FASTA_IDX@
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
19
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
20 samtools view
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
21 #if $parameter_regions.target_region == "regions_bed_file"
4
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
22 -L '$parameter_regions.regions_bed_file'
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
23 #end if
4
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
24 -@ \$addthreads
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
25 -b
5
634df184b2a8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
parents: 4
diff changeset
26 -T "\$reffa"
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
27 -o '$output_alignment'
4
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
28 input.cram
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
29 #if $parameter_regions.target_region == "region"
4
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
30 '$parameter_regions.region_string'
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
31 #end if
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
32 ]]></command>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
33
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
34 <inputs>
4
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
35 <param name="input" type="data" format="cram" label="CRAM alignment file"/>
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
36 <expand macro="mandatory_reference" argument="-t"/>
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
37 <conditional name="parameter_regions">
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
38 <param name="target_region" type="select" label="Choose conversion within specific genomic region(s)">
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
39 <option value="entire_input_file">Entire BAM alignment file</option>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
40 <option value="region">Specific region</option>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
41 <option value="regions_bed_file">List of specific regions (BED file)</option>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
42 </param>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
43 <when value="entire_input_file" />
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
44 <when value="region">
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
45 <param name="region_string" type="text" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:start-end" />
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
46 </when>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
47 <when value="regions_bed_file">
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
48 <param name="regions_bed_file" argument="-L" type="data" format="bed" label="Only include reads overlapping this BED file" />
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
49 </when>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
50 </conditional>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
51 </inputs>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
52
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
53 <outputs>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
54 <data name="output_alignment" format="bam" label="$tool.name on ${on_string}.bam"></data>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
55 </outputs>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
56
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
57 <tests>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
58 <test>
4
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
59 <param name="input" value="test.cram" ftype="cram" />
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
60 <param name="addref_select" value="history" />
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
61 <param name="ref" value="test.fa" />
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
62 <output name="output_alignment" file="test.bam" ftype="bam" lines_diff="4" />
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
63 </test>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
64 <test>
4
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
65 <param name="input" value="test.cram" ftype="cram" />
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
66 <param name="addref_select" value="history" />
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
67 <param name="ref" value="test.fa" />
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
68 <param name="target_region" value="region" />
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
69 <param name="region_string" value="CHROMOSOME_I" />
4
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
70 <output name="output_alignment" file="test.bam" ftype="bam" lines_diff="4" />
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
71 </test>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
72 <test>
4
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
73 <param name="input" value="test.cram" ftype="cram" />
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
74 <param name="addref_select" value="history" />
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
75 <param name="ref" value="test.fa" />
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
76 <param name="target_region" value="regions_bed_file" />
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
77 <param name="regions_bed_file" value="test.bed" ftype="bed" />
4
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
78 <output name="output_alignment" file="test.bam" ftype="bam" lines_diff="4" />
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
79 </test>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
80 <test>
4
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
81 <param name="input" value="test2.cram" dbkey="equCab2" ftype="cram" />
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
82 <param name="addref_select" value="cached" />
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
83 <param name="ref" value="equCab2chrM" />
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
84 <param name="target_region" value="entire_input_file" />
4
1551b0dd2d16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 3
diff changeset
85 <output name="output_alignment" file="sam_to_bam_out2.bam" ftype="bam" lines_diff="4" />
0
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
86 </test>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
87 </tests>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
88
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
89 <help><![CDATA[
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
90 **What this tool does**
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
91
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
92 Converts alignments from the CRAM format to the BAM format using the ``samtools view`` command.
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
93 ]]></help>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
94 <expand macro="citations"/>
0637018367e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
95 </tool>