Mercurial > repos > iuc > pureclip

annotate pureclip.xml @ 1:fd1f57782683 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit 169070069ea93f8cb57d660974c86baff0178b13
author iuc
date Tue, 29 May 2018 19:07:42 -0400
parents eb000bccef28
children 75bf02d7d1c8
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eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
1 <tool id="pureclip" name="PureCLIP" version="1.0.4">
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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2 <description>- HMM based peak caller designed for eCLIP/iCLIP data</description>
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
3 <requirements>
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
4 <requirement type="package" version="1.0.4">pureclip</requirement>
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
5 </requirements>
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
6 <command detect_errors="exit_code"><![CDATA[
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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7 ln -s '${target_bam_file}' target.bam &&
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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8 ln -f -s '${target_bam_file.metadata.bam_index}' target.bam.bai &&
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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9 ln -s '${genome_fasta_file}' genome.fa &&
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
10 #if $control_bam_file:
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
11 ln -s '${control_bam_file}' control.bam &&
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
12 ln -f -s '${control_bam_file.metadata.bam_index}' control.bam.bai &&
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
13 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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14 #if $motif_data.motif_data_selector == 'supply_CL_motifs':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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15 ln -s '${motif_data.cl_motif_bed_file}' motif_hits.bed &&
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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16 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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17
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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18 pureclip
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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19 -o crosslink_sites.bed
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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20 -or binding_regions.bed
1
fd1f57782683 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit 169070069ea93f8cb57d660974c86baff0178b13
iuc
parents: 0
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21 -nt \${GALAXY_SLOTS:-1}
0
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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22 -i target.bam
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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23 -bai target.bam.bai
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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24 -g genome.fa
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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25 #if $learn_params_contigs
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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26 -iv '$learn_params_contigs'
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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27 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
28 #if $apply_hmm_contigs
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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29 -iv '$apply_hmm_contigs'
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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30 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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31 -dm $merge_dist
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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32 #if $control_bam_file:
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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33 -ibam control.bam
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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34 -ibai control.bam.bai
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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35 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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36 #if $motif_data.motif_data_selector == 'supply_CL_motifs':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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37 -fis motif_hits.bed
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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38 -nim $motif_data.max_motif_id
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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39 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
40 #if $bc_data.bc_data_selector == 'bc_0':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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41 -bc 0
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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42 #elif $bc_data.bc_data_selector == 'bc_1':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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43 -bc 1
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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44 #elif $bc_data.bc_data_selector == 'manual_setting':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
45 -bw $bc_data.bandwidth
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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46 -bwn $bc_data.bandwidthn
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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47 -b1p $bc_data.b1p
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
48 -b2p $bc_data.b2p
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
49 #if $bc_data.antp_option.antp_option_selector == 'antp_select':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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50 -antp
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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51 #elif $bc_data.antp_option.antp_option_selector == 'manual_select':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
52 -ntp $bc_data.antp_option.ntp
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
53 -ntp2 $bc_data.antp_option.ntp2
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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54 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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55 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
56 #if $advanced_params.advanced_params_selector == 'ap_specify':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
57 $advanced_params.ld_precision
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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58 $advanced_params.use_viterbi
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
59 #if $advanced_params.max_iter_brent
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
60 -m $advanced_params.max_iter_brent
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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61 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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62 #if $advanced_params.max_iter_bw
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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63 -w $advanced_params.max_iter_bw
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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64 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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65 #if $advanced_params.g1kmin
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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66 -g1kmin $advanced_params.g1kmin
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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67 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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68 #if $advanced_params.g1kmax
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
69 -g1kmax $advanced_params.g1kmax
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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70 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
71 #if $advanced_params.g2kmin
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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72 -g2kmin $advanced_params.g2kmin
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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73 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
74 #if $advanced_params.g2kmax
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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75 -g2kmax $advanced_params.g2kmax
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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76 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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77 $advanced_params.fk
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
78 -mkn $advanced_params.mkn
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
79 -mtp $advanced_params.mtp
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
80 #if $advanced_params.mk
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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81 -mk $advanced_params.mk
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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82 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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83 #if $advanced_params.pa
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
84 -pa $advanced_params.pa
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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85 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
86 $advanced_params.ea1
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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87 $advanced_params.ea2
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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88 $advanced_params.et1
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
89 $advanced_params.et2
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diff changeset
90 #if $advanced_params.mrtf
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91 -mrtf $advanced_params.mrtf
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92 #end if
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93 -mtc $advanced_params.mtc
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94 -pet $advanced_params.pet
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95 #end if
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96 ]]></command>
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97 <inputs>
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98 <param name="target_bam_file" type="data" format="bam" label="Target BAM file" argument="-i"/>
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99 <param name="genome_fasta_file" type="data" format="fasta" label="Genome reference file" argument="-g"/>
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diff changeset
100 <!-- Options -->
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101 <param name="learn_params_contigs" type="text" optional="True"
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102 label="Genomic chromosomes to learn HMM parameters" argument="-iv"
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103 help="Genomic chromosomes to learn HMM parameters, e.g. 'chr1;chr2;chr3'. Contigs have to be in the same order as in BAM file. Useful to reduce runtime and memory consumption. Default: all contigs from reference file are used (useful when applying to transcript-wise alignments or poor data).">
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104 <sanitizer>
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105 <valid initial="string.printable">
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106 <remove value="&apos;"/>
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107 </valid>
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108 </sanitizer>
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109 </param>
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110 <param name="apply_hmm_contigs" type="text" label="Contigs to apply HMM" argument="-chr" optional="True"
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111 help="Contigs to apply HMM, e.g. 'chr1;chr2;chr3;'. Contigs have to be in the same order as in BAM file.">
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112 <sanitizer>
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113 <valid initial="string.printable">
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diff changeset
114 <remove value="&apos;"/>
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115 </valid>
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116 </sanitizer>
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117 </param>
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118 <param name="merge_dist" type="integer" value="8" min="1"
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119 label="Distance used to merge individual crosslink sites to binding regions" argument="-dm"/>
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120 <param name="control_bam_file" type="data" format="bam" optional="True"
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121 label="BAM file containing mapped reads from control experiment" argument="-ibam"
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122 help="Mapped reads in BAM format from a control experiment, e.g. eCLIP input"/>
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123 <conditional name="motif_data">
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124 <param name="motif_data_selector" type="select" label="Crosslink-associated (CL) motif options">
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125 <option value="no_CL_motifs_available" selected="true">No CL motifs available</option>
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126 <option value="supply_CL_motifs">Supply CL motifs</option>
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127 </param>
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128 <when value="no_CL_motifs_available" />
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129 <when value="supply_CL_motifs">
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130 <param name="cl_motif_bed_file" type="data" format="bed"
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131 label="FIMO input motif score covariates file" argument="-fis"
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132 help="FIMO input motif score covariates file"/>
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133 <param name="max_motif_id" type="integer" value="1"
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134 label="Max. motif ID to use" argument="-nim"
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diff changeset
135 help="Max. motif ID to use (Default: only covariates with motif ID 1 are used)"/>
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136 </when>
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137 </conditional>
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138
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139 <conditional name="bc_data">
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140 <param name="bc_data_selector" type="select" label="Define protein binding characteristics">
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141 <option value="bc_0" selected="true">RBP with short defined binding regions (-bc 0)</option>
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142 <option value="bc_1">RBP with larger crosslink clusters and lower read start counts (-bc 1)</option>
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143 <option value="manual_setting">Manual setting</option>
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144 </param>
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diff changeset
145 <when value="bc_0" />
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diff changeset
146 <when value="bc_1" />
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147 <when value="manual_setting">
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148 <param name="bandwidth" type="integer" value="50" min="1" max="500"
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149 label="Bandwidth for kernel density estimation used to access enrichment" argument="-bw"
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150 help="NOTE: Increasing the bandwidth increases runtime and memory consumption"/>
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151 <param name="bandwidthn" type="integer" value="50" min="1" max="500"
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152 label="Bandwidth for kernel density estimation used to estimate n for binomial distributions" argument="-bwn"
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153 help="For proteins that rather slide along the RNA or show long crosslink clusters increase -bwn, e.g. to 100 (should be LE 4*bw)"/>
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154 <param argument="-b1p" type="float" value="0.01"
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155 label="Initial value for binomial probability parameter of 'non-crosslink' state" />
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156 <param argument="-b2p" type="float" value="0.15"
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157 label="Initial value for binomial probability parameter of 'crosslink' state" />
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158 <conditional name="antp_option">
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159 <param name="antp_option_selector" type="select" label="Choose n threshold for estimating crosslink state parameters" help="Either automatically choose n threshold (-ntp, -ntp2) to estimate parameters linked to crosslink states based on expected read start count at crosslink sites, or manually set values">
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160 <option value="antp_select" selected="true">Automatically choose n threshold (-ntp, -ntp2)</option>
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161 <option value="manual_select">Manually set -ntp, -ntp2</option>
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162 </param>
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diff changeset
163 <when value="antp_select" />
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diff changeset
164 <when value="manual_select">
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165 <param argument="-ntp" type="integer" value="10"
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166 label="Only sites with n >= ntp are used to learn binomial probability parameters"/>
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167 <param argument="-ntp2" type="integer" value="0"
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168 label="Only sites with n >= ntp2 are used to learn probability of transition from state '2' to '2' or '3'"
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169 help="Useful for data with low truncation rates at crosslink sites or in general high fraction of non-coinciding read starts"/>
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170 </when>
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171 </conditional>
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172 </when>
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173 </conditional>
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174 <conditional name="advanced_params">
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175 <param name="advanced_params_selector" type="select" label="Additional advanced parameters">
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176 <option value="ap_not_specify" selected="true">Do not specify</option>
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177 <option value="ap_specify">Manually specify</option>
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178 </param>
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179 <when value="ap_not_specify" />
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180 <when value="ap_specify">
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181 <param name="ld_precision" label="Use higher precision to compute emission probabilities (long double)" type="boolean"
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182 truevalue="-ld" falsevalue="" checked="False"
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183 help="Useful in cases of extreme outliers, e.g. extreme high read start counts whose emission probabilities are close to zero and which would be discarded in default setting (along with warning messages). Note: increases memory consumption. Use in combination with '-iv' (default: double)"/>
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184 <param name="use_viterbi" label="Use Viterbi instead of posterior decoding"
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185 type="boolean" truevalue="-vtb" falsevalue="" checked="False"/>
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186 <param name="max_iter_brent" type="integer" optional="True" min="1" max="1000"
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187 label="Maximum number of iterations within BRENT algorithm" argument="-m"/>
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188 <param name="max_iter_bw" type="integer" optional="True" min="0" max="500"
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189 label="Maximum number of iterations within Baum-Welch algorithm" argument="-w"/>
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190 <param argument="-g1kmin" type="float" optional="True"
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191 label="Minimum shape k of 'non-enriched' gamma distribution" />
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192 <param argument="-g1kmax" type="float" optional="True"
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193 label="Maximum shape k of 'non-enriched' gamma distribution" />
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194 <param argument="-g2kmin" type="float" optional="True"
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195 label="Minimum shape k of 'enriched' gamma distribution" />
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196 <param argument="-g2kmax" type="float" optional="True"
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197 label="Maximum shape k of 'enriched' gamma distribution" />
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198 <param argument="-fk" label="Do not constrain 'non-enriched' shape parameter k"
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199 type="boolean" truevalue="-fk" falsevalue="" checked="False"
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200 help="When incorporating input signal, do not constrain 'non-enriched' shape parameter k LE 'enriched' gamma parameter k"/>
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201 <param argument="-mkn" type="float" value="1.0" min="0.5" max="1.5"
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202 label="Max. k/N ratio (read start sites/N) used to learn truncation probabilities for 'non-crosslink' and 'crosslink' emission probabilities"
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203 help="NOTE: high ratios might originate from mapping artifacts that can disturb parameter learning"/>
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204 <param argument="-mtp" type="float" value="0.0001"
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205 label="Min. transition probability from state '2' to '3'"
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206 help="Helpful for poor data, where no clear distinction between 'enriched' and 'non-enriched' is possible"/>
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207 <param argument="-mk" type="float" optional="True"
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208 label="Minimum KDE value used for fitting left-truncated gamma distributions"
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209 help="Default: corresponding to singleton read start."/>
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210 <param argument="-pa" type="integer" optional="True"
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211 label="Length threshold for internal poly-X stretches to get excluded" />
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212 <param argument="-ea1" label="Exclude intervals containing poly-A stretches from learning"
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213 type="boolean" truevalue="-ea1" falsevalue="" checked="False"/>
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214 <param argument="-ea2" label="Exclude intervals containing poly-A stretches from analysis"
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215 type="boolean" truevalue="-ea2" falsevalue="" checked="False"/>
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216 <param argument="-et1" label="Exclude intervals containing poly-U stretches from learning"
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217 type="boolean" truevalue="-et1" falsevalue="" checked="False"/>
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218 <param argument="-et2" label="Exclude intervals containing poly-U stretches from analysis"
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219 type="boolean" truevalue="-et2" falsevalue="" checked="False"/>
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220 <param argument="-mrtf" type="float" optional="True"
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221 label="Fit gamma shape k only for positions with min. covariate value" />
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222 <param argument="-mtc" type="integer" value="250" min="50" max="500"
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223 label="Maximum number of truncations at one position used for learning"
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224 help="NOTE: for sites with counts above threshold the whole covered regions will be ignored for learning!"/>
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225 <param argument="-pet" type="integer" value="7" min="2" max="50"
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226 label="Prior enrichment threshold"
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227 help="A KDE threshold corresponding to -pet read start counts at one position will be used for initial classification of 'non-enriched' and 'enriched' site"/>
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228 </when>
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229 </conditional>
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230 <section name="output_options" title="Additional output options">
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231 <param name="crosslink_bed_stats" type="boolean" value="False" label="Output learned parameter statistics file?"/>
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232 </section>
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233 </inputs>
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234 <outputs>
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235 <data format="bed" name="crosslink_bed_outfile" label="${tool.name} on ${on_string} crosslink sites (bed)" from_work_dir="crosslink_sites.bed"/>
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236 <data format="bed" name="binding_region_bed_outfile" label="${tool.name} on ${on_string} binding regions (bed)" from_work_dir="binding_regions.bed"/>
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237 <data format="txt" name="crosslink_bed_stats" label="${tool.name} on ${on_string} learned parameter statistcs (txt)" from_work_dir="crosslink_sites.bed.stats">
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238 <filter>(output_options['crosslink_bed_stats'] is True)</filter>
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239 </data>
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240 </outputs>
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241 <tests>
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242 <test>
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243 <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
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244 <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
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245 <param name="crosslink_bed_stats" value="True"/>
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246 <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.bed"/>
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247 <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.bed"/>
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248 <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.bed.stats"/>
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249 </test>
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250 <test>
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251 <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
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252 <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
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253 <param name="control_bam_file" value="input.aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
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254 <param name="crosslink_bed_stats" value="True"/>
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255 <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.cov_input_signal.bed"/>
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256 <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.cov_input_signal.bed"/>
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257 <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.cov_input_signal.bed.stats"/>
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258 </test>
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259 <test>
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260 <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
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261 <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
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262 <param name="motif_data_selector" value="supply_CL_motifs"/>
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263 <param name="cl_motif_bed_file" value="fimo_clmotif_occurences.chrM:4000-8300.bed" ftype="bed"/>
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264 <param name="max_motif_id" value="4"/>
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265 <param name="crosslink_bed_stats" value="True"/>
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266 <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed"/>
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267 <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.cov_CLmotifs.bed"/>
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268 <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats"/>
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269 </test>
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270 <test>
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271 <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
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272 <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
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273 <param name="control_bam_file" value="input.aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
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274 <param name="bc_data_selector" value="manual_setting"/>
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275 <param name="bandwidthn" value="50"/>
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276 <param name="b1p" value="0.01"/>
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277 <param name="b2p" value="0.15"/>
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278 <param name="antp_option_selector" value="manual_select"/>
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279 <param name="ntp" value="10"/>
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280 <param name="ntp2" value="0"/>
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281 <param name="advanced_params_selector" value="ap_specify"/>
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282 <param name="fk" value="True"/>
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283 <param name="mkn" value="0.9"/>
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284 <param name="mtc" value="200"/>
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285 <param name="crosslink_bed_stats" value="True"/>
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286 <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.test4.bed"/>
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287 <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.test4.bed"/>
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288 <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.test4.bed.stats"/>
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289 </test>
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290 </tests>
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291 <help><![CDATA[
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292
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293 PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP. It accepts mapped eCLIP/iCLIP reads in BAM format as input and also supports control library and crosslink-associated (CL) motifs input for bias correction.
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294
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295 PureCLIP outputs two BED files, containing the found crosslink sites (first file) and binding regions (second file) that merge nearby crosslink sites to contiguous regions (region width controlled by -dm parameter).
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296
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297 By default, the tool parameters are set to values optimized for proteins binding to short defined binding regions, e.g. proteins binding to short specific motifs such as PUM2 and RBFOX2. This behaviour can be changed with the -bc option. The default setting -bc 0 is equivalent to manually setting -bdwn 50 -ntp 10 -ntp2 0 -b1p 0.01 -b2p 0.15. The second setting -bc 1 is designed for RBPs that produce larger clusters (proteins causing larger crosslink clusters with relatively lower read start counts, e.g. proteins binding to low complexity motifs). -bc 1 corresponds to the manual setting -bdwn 100 -antp -b2p 0.01 -b2p 0.1.
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298
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299 In case of different binding characteristics, you can manually adjust parameters -bdw, -bdwn, -b1p, -b2p, -antp or have a look at the online documentation for more details:
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300
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301 http://pureclip.readthedocs.io/en/latest/index.html
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302
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303 ]]></help>
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304 <citations>
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305 <citation type="doi">10.1186/s13059-017-1364-2</citation>
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306 </citations>
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307 </tool>