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remove tool show_in_ucsc
This commit is contained in:
Jianbin He
@@ -1,65 +0,0 @@
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#!/usr/bin/env python2.4
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"""
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Tool to display multiple datasets at the UCSC genome browser at a time, along with their custom track details.
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Done by: Guru
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"""
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import sys,os
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primary = sys.argv[2]
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color_list = [sys.argv[3].replace('-',',')]
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visib_list = [sys.argv[4]]
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if sys.argv[5]:
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for color in sys.argv[5].split(','):
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color_list.append(color.replace('-',','))
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if sys.argv[6]:
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visib_list.extend(sys.argv[6].split(","))
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#visib_list = [sys.argv[4], sys.argv[6]]
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input_list = []
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input_list.append(primary)
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name_list = [sys.argv[7].replace("_NAME_","").replace("_SPACE_"," ").replace("_OPEN_","(").replace("_CLOSE_",")")]
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i=8
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for item in sys.argv[8:]:
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if item.count("_NAME_") != 0 or item == "customTrack2.bed":
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item=item.replace("_NAME_","").replace("_SPACE_"," ").replace("_OPEN_","(").replace("_CLOSE_",")")
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for sym in ["(u__sq__","u__sq__","__sq__,","__sq__)","__sq__","__ob__", "__cb__"]:
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item = item.replace(sym, "")
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name_list.append(item)
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i+=1
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else:
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break
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for item in sys.argv[i:]:
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if item.count("/") == 0:
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item = item.replace(',','').replace("]",'').replace("[","")
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try:
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assert int(item)
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item = "./database/files/dataset_" + item + ".dat"
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except:
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pass
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input_list.append(item)
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out=[]
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if color_list[1] == 'None':
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color_list.pop()
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visib_list.pop()
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j=1
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while j < len(input_list):
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color_list.append('0,0,0')
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visib_list.append('1')
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j+=1
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fout = open(sys.argv[1],"w")
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for k,inp in enumerate(input_list):
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print >>fout, "track name='%s' visibility=%d color=%s" %(name_list[k],int(visib_list[k]),color_list[k])
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print >>fout, open(inp,"r").read()
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fout.close()
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print "Display %d tracks in UCSC" %(len(input_list))
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@@ -1,98 +0,0 @@
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<tool id="show_in_ucsc" name="Display customtrack at UCSC">
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<description>displays selected datasets in the UCSC genome browser</description>
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<command interpreter="python2.4">show_in_ucsc.py $out_file1 $primary $primary_color $primary_visib $Color $Visibility $primary_name $other_names $newdata</command>
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<inputs>
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<page>
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<param format="interval" label="Choose primary dataset" name="primary" type="data" />
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<param label="Color" name="primary_color" type="select">
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<option selected="yes" value="0-0-0">Black</option>
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<option value="255-0-0">Red</option>
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<option value="0-255-0">Green</option>
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<option value="0-0-255">Blue</option>
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<option value="255-0-255">Magenta</option>
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<option value="0-255-255">Cyan</option>
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<option value="255-215-0">Gold</option>
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<option value="160-32-240">Purple</option>
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<option value="255-140-0">Orange</option>
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<option value="255-20-147">Pink</option>
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<option value="92-51-23">Dark Chocolate</option>
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<option value="85-107-47">Olive green</option>
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</param>
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<param label="Visibility" name="primary_visib" type="select">
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<option selected="yes" value="1">Dense</option>
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<option value="2">Full</option>
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<option value="3">Pack</option>
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<option value="4">Squish</option>
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<option value="0">Hide</option>
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</param>
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</page>
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<page>
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<param name="newdata" type="data" label="Choose datasets" multiple="true" dynamic_options = " print_out(primary) " />
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<param label="Change attributes?" name="status" type="select">
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<option value="0" selected="yes"> No </option>
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<option value="1"> Yes </option>
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</param>
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<param type="hidden" name="primary_name" value="hello" dynamic_options = "print_name(primary)"/>
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</page>
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<page>
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<param name="Color" type="select" condition= "status" repeat= "newdata">
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<option selected="yes" value="0-0-0">Black</option>
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<option value="255-0-0">Red</option>
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<option value="0-255-0">Green</option>
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<option value="0-0-255">Blue</option>
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<option value="255-0-255">Magenta</option>
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<option value="0-255-255">Cyan</option>
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<option value="255-215-0">Gold</option>
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<option value="160-32-240">Purple</option>
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<option value="255-140-0">Orange</option>
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<option value="255-20-147">Pink</option>
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<option value="92-51-23">Dark Chocolate</option>
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<option value="85-107-47">Olive green</option>
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</param>
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<param name="Visibility" type="select" condition= "status" repeat= "with_Color">
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<option selected="yes" value="1">Dense</option>
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<option value="2">Full</option>
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<option value="3">Pack</option>
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<option value="4">Squish</option>
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<option value="0">Hide</option>
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</param>
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<param type="hidden" name="other_names" dynamic_options = "print_name(newdata)"/>
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</page>
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</inputs>
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<outputs>
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<data format="customtrack" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="primary" value="customTrack1.bed" />
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<param name="primary_color" value="0-0-0" />
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<param name="primary_visib" value="1" />
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<param name="primary_name" value="customTrack1.bed" />
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<param name="newdata" value="customTrack2.bed" />
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<param name="status" value="1" />
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<param name="Color" value="255-0-0" />
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<param name="Visibility" value="2" />
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<param name="other_names" value="customTrack2.bed" />
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<output name="out_file1" file="customTrack_output.dat" />
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</test>
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</tests>
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<help>
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**Info**
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This tool displays the selected datasets with their custom track attributes (if any) in the UCSC genome browser.
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This tool allows you to set the **Color** and **Visibility** attributes and you can edit the **Name** attribute of the dataset by clicking on **"edit attributes"** button (pencil icon) next to the dataset name in the history panel.
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Please note that the primary dataset in step 1 of the tool sets the database build for the datasets in step 2.
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</help>
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<code file="show_in_ucsc_code.py" />
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</tool>
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@@ -1,17 +0,0 @@
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import os, sys
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def print_out(data):
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build = str(data.dbkey)
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id = data.id
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extension = ["bed", "interval"]
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return (build,id,extension)
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def print_name(data):
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if isinstance(data, list):
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name_list=[]
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for item in data:
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name_list.append("_NAME_" + item.name.replace("(","_OPEN_").replace(")","_CLOSE_").replace(" ","_SPACE_"))
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return name_list
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else:
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return "_NAME_" + data.name.replace("(","_OPEN_").replace(")","_CLOSE_").replace(" ","_SPACE_")
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