Mercurial > repos > iuc > macs2
comparison macs2_predictd.xml @ 18:640d3af5d833 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
author | iuc |
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date | Sat, 02 Apr 2022 21:37:38 +0000 |
parents | 424aefbd7777 |
children | 86e2413cf3f8 |
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17:424aefbd7777 | 18:640d3af5d833 |
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1 <tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.1"> | 1 <tool id="macs2_predictd" name="MACS2 predictd" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> |
2 <description>Predict 'd' or fragment size from alignment results</description> | 2 <description>Predict 'd' or fragment size from alignment results</description> |
3 <expand macro="bio_tools"/> | |
3 <macros> | 4 <macros> |
4 <import>macs2_macros.xml</import> | 5 <import>macs2_macros.xml</import> |
5 </macros> | 6 </macros> |
6 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
7 <expand macro="stdio" /> | 8 <expand macro="stdio" /> |
13 -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) } | 14 -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) } |
14 @tag_size@ | 15 @tag_size@ |
15 @effective_genome_size@ | 16 @effective_genome_size@ |
16 --bw '${ band_width }' | 17 --bw '${ band_width }' |
17 @mfold_command@ | 18 @mfold_command@ |
19 --d-min $d_min | |
20 @buffer_size@ | |
18 | 21 |
19 ## remove the timepoint and strip the output | 22 ## remove the timepoint and strip the output |
20 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1' | 23 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1' |
21 | 24 |
22 > '${ outfile }' | 25 > '${ outfile }' |
31 help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" /> | 34 help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" /> |
32 <expand macro="conditional_effective_genome_size" /> | 35 <expand macro="conditional_effective_genome_size" /> |
33 <expand macro="tag_size" /> | 36 <expand macro="tag_size" /> |
34 <expand macro="band_width" /> | 37 <expand macro="band_width" /> |
35 <expand macro="mfold_options" /> | 38 <expand macro="mfold_options" /> |
39 <expand macro="fragment_size"/> | |
40 <expand macro="buffer_size"/> | |
36 </inputs> | 41 </inputs> |
37 | 42 |
38 <outputs> | 43 <outputs> |
39 <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" /> | 44 <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" /> |
40 <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" /> | 45 <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" /> |
46 <param name="gsize" value="3300000000" /> | 51 <param name="gsize" value="3300000000" /> |
47 <param name="tsize" value=""/> | 52 <param name="tsize" value=""/> |
48 <param name="band_width" value="300"/> | 53 <param name="band_width" value="300"/> |
49 <param name="lower" value="5"/> | 54 <param name="lower" value="5"/> |
50 <param name="upper" value="50"/> | 55 <param name="upper" value="50"/> |
56 <assert_command> | |
57 <has_text text="--buffer-size"/> | |
58 <has_text text="--d-min"/> | |
59 </assert_command> | |
51 <output name="outfile"> | 60 <output name="outfile"> |
52 <assert_contents> | 61 <assert_contents> |
53 <has_line line="# predicted fragment length is 284 bps" /> | 62 <has_line line="# predicted fragment length is 284 bps" /> |
54 </assert_contents> | 63 </assert_contents> |
55 </output> | 64 </output> |
56 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/> | 65 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size" ftype="pdf"/> |
57 </test> | 66 </test> |
58 </tests> | 67 </tests> |
59 <help> | 68 <help> |
60 <![CDATA[ | 69 <![CDATA[ |
61 **What it does** | 70 **What it does** |