Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/screen.seqs.xml @ 32:ec8df51e841a
Fixes courtesy of Peter Briggs:
metagenomics.py:
- Groups class: Fix for when second column not present
- Axes class: make 'sniff' method more sensitive to try and restrict arbitrary tabular
data uploads being sniffed as this type
mothur_wrapper.py:
- update cmd_dict['chimera.perseus'], to use correct inputs
- add --beta option (needed for chimera.perseus tool)
- add function for converting input floats from scientific notation (e.g. 1e-6,
which mothur can't handle) to decimal format (e.g. 0.00001, which it can)
chimera.perseus.xml:
- add output data item for the "accnos" file (not previous captured in the
history)
trim.flows.xml:
- cosmetic change: base name for additional output data items is now "trim.flows",
rather than "logfile" (clarifies history items)
shhh.flows.xml:
- cosmetic change: update default value specified in help for mindiff to be
consistent with that given in the mothur documentation
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 04 Sep 2013 10:51:34 -0500 |
parents | a3eed59297ea |
children | 95d75b35e4d2 |
rev | line source |
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1 <tool id="mothur_screen_seqs" name="Screen.seqs" version="1.23.0"> |
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2 <description>Screen sequences</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 #import re, os.path |
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6 --cmd='screen.seqs' |
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7 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] |
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8 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_fasta.__str__)) + ":'" + $out_file.__str__] |
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9 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.bad.accnos',$os.path.basename($input_fasta.__str__)) + ":'" + $bad_accnos.__str__] |
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10 --outputdir='$logfile.extra_files_path' |
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11 --tmpdir='${logfile.extra_files_path}/input' |
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12 --fasta=$input_fasta |
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13 #if int($start) >= 0: |
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14 --start=$start |
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15 #end if |
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16 #if int($end) >= 0: |
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17 --end=$end |
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18 #end if |
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19 #if int($minlength) >= 0: |
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20 --minlength=$minlength |
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21 #end if |
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22 #if int($maxlength) >= 0: |
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23 --maxlength=$maxlength |
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24 #end if |
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25 #if int($maxambig) >= 0: |
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26 --maxambig=$maxambig |
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27 #end if |
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28 #if int($maxhomop) >= 0: |
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29 --maxhomop=$maxhomop |
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30 #end if |
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31 #if int($criteria) >= 0: |
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32 --criteria=$criteria |
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33 #end if |
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34 #if $optimize != None and $optimize.__str__ != "None": |
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35 --optimize=$optimize |
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36 #end if |
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37 #if $input_qfile != None and $input_qfile.__str__ != "None": |
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38 --qfile=$input_qfile |
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39 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_qfile.__str__)) + ":'" + $output_qfile.__str__] |
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40 #end if |
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41 #if $input_names != None and $input_names.__str__ != "None": |
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42 --name=$input_names |
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43 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_names.__str__)) + ":'" + $output_names.__str__] |
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44 #end if |
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45 #if $input_groups != None and $input_groups.__str__ != "None": |
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46 --group=$input_groups |
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47 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_groups.__str__)) + ":'" + $output_groups.__str__] |
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48 #end if |
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49 #if $input_alignreport != None and $input_alignreport.__str__ != "None": |
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50 --alignreport=$input_alignreport |
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51 ###set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_alignreport.__str__)) + ":'" + $output_alignreport.__str__] |
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52 #set results = $results + ["'^\S+\.good\.align\.report$:'" + $output_alignreport.__str__] |
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53 #end if |
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54 #if $input_taxonomy != None and $input_taxonomy.__str__ != "None": |
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55 --taxonomy=$input_taxonomy |
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56 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_taxonomy.__str__)) + ":'" + $output_taxonomy.__str__] |
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57 #end if |
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58 --result=#echo ','.join($results) |
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59 --processors=8 |
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60 </command> |
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61 <inputs> |
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62 <param name="input_fasta" type="data" format="fasta,align" label="fasta - Fasta to screen"/> |
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63 <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/> |
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64 <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/> |
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65 <param name="minlength" type="integer" value="-1" label="minlength - Remove sequences shorter than (ignored when negative)"/> |
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66 <param name="maxlength" type="integer" value="-1" label="maxlength - Remove sequences longer than (ignored when negative)"/> |
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67 <param name="maxambig" type="integer" value="-1" label="maxambig - Remove sequences with ambiguous bases greater than (ignored when negative)"/> |
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68 <param name="maxhomop" type="integer" value="-1" label="maxhomop - Remove sequences with homopolymers greater than (ignored when negative)"/> |
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69 <param name="criteria" type="integer" value="-1" label="criteria - Percent of sequences that an optimize value must match to be retained(ignored when negative)"/> |
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70 <param name="optimize" type="select" multiple="true" display="checkboxes" label="optimize - Optimize selected paramenters"> |
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71 <option value="start">start</option> |
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72 <option value="end">end</option> |
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73 <option value="minlength">minlength</option> |
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74 <option value="maxlength">maxlength</option> |
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75 <option value="maxambig">maxambig</option> |
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76 <option value="maxhomop">maxhomop</option> |
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77 </param> |
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78 <param name="input_qfile" type="data" format="qual" optional="true" label="qfile - Sequence Quality file to screen"/> |
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79 <param name="input_names" type="data" format="names" optional="true" label="name - Sequence Names to screen"/> |
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80 <param name="input_groups" type="data" format="groups" optional="true" label="group - Groups to screen"/> |
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81 <param name="input_alignreport" type="data" format="align.report" optional="true" label="alignreport - Align Report to screen"/> |
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82 <param name="input_taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/> |
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83 </inputs> |
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84 <outputs> |
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85 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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86 <data format_source="input_fasta" name="out_file" label="${tool.name} on ${on_string}: good.${input_fasta.datatype.file_ext}" /> |
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87 <data format="accnos" name="bad_accnos" label="${tool.name} on ${on_string}: bad.accnos" /> |
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88 <data format_source="input_qfile" name="output_qfile" label="${tool.name} on ${on_string}: qfile" > |
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89 <filter>input_qfile != None</filter> |
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90 </data> |
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91 <data format="names" name="output_names" label="${tool.name} on ${on_string}: names" > |
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92 <filter>input_names != None</filter> |
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93 </data> |
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94 <data format="groups" name="output_groups" label="${tool.name} on ${on_string}: groups" > |
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95 <filter>input_groups != None</filter> |
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96 </data> |
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97 <data format="align.report" name="output_alignreport" label="${tool.name} on ${on_string}: align.report" > |
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98 <filter>input_alignreport != None</filter> |
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99 </data> |
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100 <data format="taxonomy" name="output_taxonomy" label="${tool.name} on ${on_string}: taxonomy" > |
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101 <filter>input_taxonomy != None</filter> |
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102 </data> |
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103 </outputs> |
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104 <requirements> |
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105 <requirement type="package" version="1.27">mothur</requirement> |
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106 </requirements> |
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107 <tests> |
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108 </tests> |
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109 <help> |
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110 **Mothur Overview** |
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111 |
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112 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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113 in the Department of Microbiology and Immunology at The University of Michigan, |
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114 provides bioinformatics for the microbial ecology community. |
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115 |
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116 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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117 |
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118 **Command Documenation** |
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119 |
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120 The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a name_, group_, or align.report_ file. |
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121 |
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122 .. _name: http://www.mothur.org/wiki/Name_file |
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123 .. _group: http://www.mothur.org/wiki/Group_file |
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124 .. _align.report: http://www.mothur.org/wiki/Align.seqs |
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125 .. _screen.seqs: http://www.mothur.org/wiki/Screen.seqs |
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126 |
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127 |
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128 </help> |
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129 </tool> |