Mercurial > repos > bgruening > hicexplorer_hicdifferentialtad
comparison hicDifferentialTAD.xml @ 2:77d8e0fd162a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
| author | iuc |
|---|---|
| date | Wed, 18 Oct 2023 11:06:49 +0000 |
| parents | 608538d083a2 |
| children |
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| 1:608538d083a2 | 2:77d8e0fd162a |
|---|---|
| 28 --threads @THREADS@ | 28 --threads @THREADS@ |
| 29 | 29 |
| 30 ]]> | 30 ]]> |
| 31 </command> | 31 </command> |
| 32 <inputs> | 32 <inputs> |
| 33 <param name='matrix_h5_cooler_target' type="data" format="h5,cool" label="Target matrix to compute on" /> | 33 <param name="matrix_h5_cooler_target" type="data" format="h5,cool" label="Target matrix to compute on" /> |
| 34 <param name='matrix_h5_cooler_control' type="data" format="h5,cool" label="Control matrix to compute on" /> | 34 <param name="matrix_h5_cooler_control" type="data" format="h5,cool" label="Control matrix to compute on" /> |
| 35 | 35 |
| 36 <param argument="--tadDomains" type="data" format='bed' optional='false' label="TAD domains file" help= "The TADs domain file computed by hicFindTADs." /> | 36 <param argument="--tadDomains" type="data" format="bed" optional="false" label="TAD domains file" help= "The TADs domain file computed by hicFindTADs." /> |
| 37 <param argument="--pValue" type="float" label="P-value" min='0.0' max='1.0' help= "H0 is considered as \'two regions are identical.\' i.e. all regions with a test result of smaller p-value are rejected and considered as differential." value='0.05' /> | 37 <param argument="--pValue" type="float" label="P-value" min="0.0" max="1.0" help= "H0 is considered as \'two regions are identical.\' i.e. all regions with a test result of smaller p-value are rejected and considered as differential." value="0.05" /> |
| 38 <param name="mode_selector" type="select" label="Method to compute the differentail TAD expression"> | 38 <param name="mode_selector" type="select" label="Method to compute the differentail TAD expression"> |
| 39 <option value="intra-TAD">intra-TAD</option> | 39 <option value="intra-TAD">intra-TAD</option> |
| 40 <option value="left-inter-TAD">left-inter-TAD</option> | 40 <option value="left-inter-TAD">left-inter-TAD</option> |
| 41 <option value="right-inter-TAD">right-inter-TAD</option> | 41 <option value="right-inter-TAD">right-inter-TAD</option> |
| 42 <option value="all" selected="True">all</option> | 42 <option value="all" selected="True">all</option> |
| 46 <option value="one" selected="True">one</option> | 46 <option value="one" selected="True">one</option> |
| 47 <option value="all">all</option> | 47 <option value="all">all</option> |
| 48 </param> | 48 </param> |
| 49 </inputs> | 49 </inputs> |
| 50 <outputs> | 50 <outputs> |
| 51 <data name='acceptedTADs' from_work_dir='galaxy_differential_tad_accepted.diff_tad' format='txt' label='Accepted TADs' /> | 51 <data name="acceptedTADs" from_work_dir="galaxy_differential_tad_accepted.diff_tad" format="txt" label="Accepted TADs" /> |
| 52 <data name='rejectedTADs' from_work_dir='galaxy_differential_tad_rejected.diff_tad' format='txt' label='Rejected TADs' /> | 52 <data name="rejectedTADs" from_work_dir="galaxy_differential_tad_rejected.diff_tad" format="txt" label="Rejected TADs" /> |
| 53 </outputs> | 53 </outputs> |
| 54 <tests> | 54 <tests> |
| 55 <test> | 55 <test> |
| 56 <param name="matrix_h5_cooler_target" value="small_test_matrix.cool" /> | 56 <param name="matrix_h5_cooler_target" value="small_test_matrix.cool" /> |
| 57 <param name="matrix_h5_cooler_control" value="small_test_matrix.cool" /> | 57 <param name="matrix_h5_cooler_control" value="small_test_matrix.cool" /> |
| 58 | 58 |
| 59 <param name="tadDomains" ftype='bed' value="hicDifferentialTAD/multiNone_domains.bed" /> | 59 <param name="tadDomains" ftype="bed" value="hicDifferentialTAD/multiNone_domains.bed" /> |
| 60 <param name="pValue" value="1.0" /> | 60 <param name="pValue" value="1.0" /> |
| 61 <param name="mode_selector" value="all" /> | 61 <param name="mode_selector" value="all" /> |
| 62 <param name="modeReject" value="one" /> | 62 <param name="modeReject" value="one" /> |
| 63 <output name="acceptedTADs" file="hicDifferentialTAD/accepted.txt" ftype="txt" /> | 63 <output name="acceptedTADs" file="hicDifferentialTAD/accepted.txt" ftype="txt" /> |
| 64 <!-- TODO remove lines_diff when updating to >=3.7 where" a multicore issue was solved that led to skipping data at the start and end of chromosomes--> | 64 <!-- TODO remove lines_diff when updating to >=3.7 where" a multicore issue was solved that led to skipping data at the start and end of chromosomes--> |